Methods of producing 6-carbon chemicals via methyl-ester shielded carbon chain elongation

ABSTRACT

This document describes biochemical pathways for producing adipic acid, 6-aminohexanoic acid, 6-hydroxhexanoic acid, hexamethylenediamine, caprolactam, or 1,6-hexanediol by forming one or two terminal functional groups, comprised of carboxyl, amine or hydroxyl group, in a C6 aliphatic backbone substrate. These pathways, metabolic engineering and cultivation strategies described herein rely on the enzymes or homologs accepting methyl ester shielded dicarboxylic acid substrates.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority of U.S. Provisional Application Ser.No. 61/747,454, filed Dec. 31, 2012, and U.S. Provisional ApplicationSer. No. 61/829,163, filed May 30, 2013. The contents of the priorapplications are incorporated herein by reference in their entirety.

TECHNICAL FIELD

This invention relates to methods for biosynthesizing one or more ofadipic acid, 6-aminohexanoic acid, 6-hydroxhexanoic acid,hexamethylenediamine, caprolactam, and 1,6-hexanediol (hereafter “C6building blocks”) from oxalyl-CoA and either (i) malonyl-CoA or (ii)malonyl-[acp] and acetyl-CoA using one or more isolated enzymes such asmethyltransferases, β-ketoacyl-[acp] synthases, β-ketothiolases,dehydrogenases, reductases, hydratases, thioesterases, methylesterases,CoA-transferases, reversible CoA-ligases and transaminases or usingrecombinant host cells expressing one or more such enzymes.

BACKGROUND

Nylons are polyamides that are generally synthesized by the condensationpolymerisation of a diamine with a dicarboxylic acid. Similarly, Nylonsmay be produced by the condensation polymerization of lactams. Aubiquitous Nylon is Nylon 6,6, which is produced by reaction ofhexamethylenediamine (HMD) and adipic acid. Nylon 6 can be produced by aring opening polymerization of caprolactam. Therefore, adipic acid,hexamethylenediamine and caprolactam are important intermediates in theproduction of Nylons (Anton & Baird, Polyamides Fibers, Encyclopedia ofPolymer Science and Technology, 2001).

Industrially, adipic acid and caprolactam are produced via air oxidationof cyclohexane. The air oxidation of cyclohexane produces, in a seriesof steps, a mixture of cyclohexanone (K) and cyclohexanol (A),designated as KA oil. Nitric acid oxidation of KA oil produces adipicacid (Musser, Adipic acid, Ullmann's Encyclopedia of IndustrialChemistry, 2000). Caprolactam is produced from cyclohexanone via itsoxime and subsequent acid rearrangement (Fuchs, Kieczka and Moran,Caprolactam, Ullmann's Encyclopedia of Industrial Chemistry, 2000)

Industrially, hexamethylenediamine (HMD) is produced by hydrocyanationof C6 building block to adiponitrile, followed by hydrogenation to HMD(Herzog and Smiley, Hexamethylenediamine, Ullmann's Encyclopedia ofIndustrial Chemistry, 2012).

Given a reliance on petrochemical feedstocks; biotechnology offers analternative approach via biocatalysis. Biocatalysis is the use ofbiological catalysts, such as enzymes, to perform biochemicaltransformations of organic compounds.

Both bioderived feedstocks and petrochemical feedstocks are viablestarting materils for the biocatalysis processes.

Accordingly, against this background, it is clear that there is a needfor sustainable methods for producing one or more of adipic acid,caprolactam, 6-aminohexanoic acid, 6-hydroxyhexanoic acid,hexamethylenediamine, and 1,6-hexanediol (hereafter “C6 buildingblocks”) wherein the methods are biocatalyst based (Jang et al.,Biotechnol. Bioeng., 2012, 109(10), 2437-2459).

However, no wild-type prokaryote or eukaryote naturally overproduces orexcretes C6 building blocks to the extracellular environment.Nevertheless, the metabolism of adipic acid and caprolactam has beenreported (Ramsay et al., Appl. Environ. Microbiol., 1986, 52(1),152-156; and Kulkarni and Kanekar, Current Microbiology, 1998, 37,191-194).

The dicarboxylic acid, adipic acid, is converted efficiently as a carbonsource by a number of bacteria and yeasts via β-oxidation into centralmetabolites. β-oxidation of Coenzyme A (CoA) activated adipate to CoAactivated 3-oxoadipate facilitates further catabolism via, for example,pathways associated with aromatic substrate degradation. The catabolismof 3-oxoadipyl-CoA to acetyl-CoA and succinyl-CoA by several bacteriaand fungi has been characterized comprehensively (Harwood and Parales,Annual Review of Microbiology, 1996, 50, 553-590). Both adipate and6-aminohexanoate are intermediates in the catabolism of caprolactam,finally degraded via 3-oxoadipyl-CoA to central metabolites.

Potential metabolic pathways have been suggested for producing adipicacid from biomass-sugar: (1) biochemically from glucose to cis,cismuconic acid via the ortho-cleavage aromatic degradation pathway,followed by chemical catalysis to adipic acid; (2) a reversible adipicacid degradation pathway via the condensation of succinyl-CoA andacetyl-CoA and (3) combining β-oxidation, a fatty acid synthase andw-oxidation. However, no information using these strategies has beenreported (Jang et al., Biotechnology & Bioengineering, 2012, 109(10),2437-2459).

The optimality principle states that microorganisms regulate theirbiochemical networks to support maximum biomass growth. Beyond the needfor expressing heterologous pathways in a host organism, directingcarbon flux towards C6 building blocks that serve as carbon sourcesrather than as biomass growth constituents, contradicts the optimalityprinciple. For example, transferring the 1-butanol pathway fromClostridium species into other production strains has often fallen shortby an order of magnitude compared to the production performance ofnative producers (Shen et al., Appl. Environ. Microbiol., 2011, 77(9),2905-2915).

The efficient synthesis of the six carbon aliphatic backbone precursoris a key consideration in synthesizing C6 building blocks prior toforming terminal functional groups, such as carboxyl, amine or hydroxylgroups, on the C6 aliphatic backbone.

SUMMARY

This document is based at least in part on the discovery that it ispossible to construct biochemical pathways for producing a six carbonchain aliphatic backbone precursor, in which one or two functionalgroups, i.e., carboxyl, amine, or hydroxyl, can be formed, leading tothe synthesis of one or more of adipic acid, 6-aminohexanoate,6-hydroxhexanoate, hexamethylenediamine, caprolactam, and 1,6-hexanediol(hereafter “C6 building blocks). Adipic acid and adipate,6-hydroxhexanoic acid and 6-hydroxhexanoate, and 6-aminohexanoic and6-aminohexanoate are used interchangeably herein to refer to thecompound in any of its neutral or ionized forms, including any saltforms thereof. It is understood by those skilled in the art that thespecific form will depend on pH. These pathways, metabolic engineeringand cultivation strategies described herein rely on fatty acidelongation and synthesis enzymes or homologs accepting methyl-estershielded dicarboxylic acids as substrates.

In the face of the optimality principle, it surprisingly has beendiscovered that appropriate non-natural pathways, feedstocks, hostmicroorganisms, attenuation strategies to the host's biochemical networkand cultivation strategies may be combined to efficiently produce one ormore C6 building blocks.

In some embodiments, the C6 aliphatic backbone for conversion to one ormore C6 building blocks is adipyl-[acp] or adipyl-CoA (also known as6-carboxyhexanoyl-CoA), which can be formed from oxalyl-CoA andmalonyl-[acp], malonyl-CoA, or acetyl-CoA, via two cycles of carbonchain elongation using either NADH or NADPH dependent enzymes. See FIG.1A, FIG. 1B and FIG. 1C.

In some embodiments, a terminal carboxyl group can be enzymaticallyformed using a pimeloyl-[acp] methyl ester methylesterase, athioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoatedehydrogenase, a 6-oxohexanoate dehydrogenase, a reversible CoA ligase(e.g., reversible succinyl-CoA ligase) or a CoA-transferase (e.g., aglutaconate CoA-transferase). See FIG. 1A, FIG. 1B, FIG. 1C and FIG. 2.

In some embodiments, a terminal amine group can be enzymatically formedusing a ω-transaminase or a deacetylase. See FIG. 3 and FIG. 4.

In some embodiments, a terminal hydroxyl group can be enzymaticallyformed using a 4-hydroxybutyrate dehydrogenase, 5-hydroxypentanoatedehydrogenase or a 6-hydroxyhexanoate dehydrogenase or an alcoholdehydrogenase. See FIG. 5 and FIG. 6.

In one aspect, this document features a method for biosynthesizing aproduct selected from the group consisting of adipic acid,6-aminohexanoate, 6-hydroxhexanoate, hexamethylenediamine, caprolactam,and 1,6-hexanediol. The method includes enzymatically synthesizing a sixcarbon chain aliphatic backbone from oxalyl-CoA and either (i)acetyl-CoA or malonyl-CoA via two cycles of methyl ester shielded carbonchain elongation or (ii) malonyl-[acp] via two cycles of methyl-estershielded carbon chain elongation, and enzymatically forming one or twoterminal functional groups selected from the group consisting ofcarboxyl, amine, and hydroxyl groups in the backbone, thereby formingthe product. The six carbon chain aliphatic backbone can be adipyl-[acp]or adipyl-CoA. A malonyl-[acp] O-methyltransferase can convertoxalyl-CoA to oxalyl-CoA methyl ester. Each of the two cycles of carbonchain elongation can include using (i) a β-ketoacyl-[acp] synthase or aβ-ketothiolase, (ii) a 3-oxoacyl-[acp] reductase, an acetoacetyl-CoAreductase, a 3-hydroxyacyl-CoA dehydrogenase or a 3-hydroxybutyryl-CoAdehydrogenase, (iii) an enoyl-CoA hydratase or a 3-hydroxyacyl-[acp]dehydratase, and (iv) an enoyl-[acp] reductase or a trans-2-enoyl-CoAreductase to produce adipyl-[acp] methyl ester or adipyl-[acp] methylester. A pimeloyl-[acp] methyl ester methylesterase can remove themethyl group from adipyl-CoA methyl ester or adipyl-[acp] methyl ester.The malonyl-[acp]O-methyltransferase can have at least 70% sequenceidentity to the amino acid sequence set forth in SEQ ID NO: 16. Thepimeloyl-[acp] methyl ester methylesterase can have at least 70%sequence identity to the amino acid sequence set forth in SEQ ID NO: 17.

The two terminal functional groups can be the same (e.g., amine orhydroxyl) or can be different (e.g., a terminal amine and a terminalcarboxyl group; or a terminal hydroxyl group and a terminal carboxylgroup).

A ω-transaminase or a deacetylase can enzymatically form an amine group.The ω-transaminase can have at least 70% sequence identity to any one ofthe amino acid sequences set forth in SEQ ID NO. 8-13.

A 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase,a 4-hydroxybutyrate dehydratase, or an alcohol dehydrogenase canenzymatically form a hydroxyl group.

A thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoatedehydrogenase, a 6-oxohexanoate dehydrogenase, a CoA-transferase (e.g. aglutaconate CoA transferase), or a reversible CoA-ligase (e.g., areversible succinate-CoA ligase) can enzymatically forms a terminalcarboxyl group. The thioesterase can have at least 70% sequence identityto the amino acid sequence set forth in SEQ ID NO: 1.

A carboxylate reductase and a phosphopantetheinyl transferase can form aterminal aldehyde group as an intermediate in forming the product. Thecarboxylate reductase can have at least 70% sequence identity to any oneof the amino acid sequences set forth in SEQ ID NO. 2-7.

Any of the methods can be performed in a recombinant host byfermentation. The host can be subjected to a cultivation strategy underaerobic, anaerobic, micro-aerobic or mixed oxygen/denitrificationcultivation conditions. The host can be cultured under conditions ofnutrient limitation. The host can be retained using a ceramic hollowfiber membrane to maintain a high cell density during fermentation.

In any of the methods, the host's tolerance to high concentrations of aC6 building block can be improved through continuous cultivation in aselective environment.

The principal carbon source fed to the fermentation can derive frombiological or non-biological feedstocks. In some embodiments, thebiological feedstock is, includes, or derives from, monosaccharides,disaccharides, lignocellulose, hemicellulose, cellulose, lignin,levulinic acid and formic acid, triglycerides, glycerol, fatty acids,agricultural waste, condensed distillers' solubles, or municipal waste.

In some embodiments, the non-biological feedstock is or derives fromnatural gas, syngas, CO₂/H₂, methanol, ethanol, benzoate, non-volatileresidue (NVR) or a caustic wash waste stream from cyclohexane oxidationprocesses, or a terephthalic acid/isophthalic acid mixture waste stream.

This document also features a recombinant host that includes at leastone exogenous nucleic acid encoding (i) a malonyl-[acp]O-methyltransferase, (ii) a β-ketoacyl-[acp] synthase or aβ-ketothiolase, (iii) a 3-oxoacyl-[acp] reductase, acetoacetyl-CoAreductase, a 3-hydroxyacyl-CoA dehydrogenase or a 3-hydroxybutyryl-CoAdehydrogenase, (iv) an enoyl-CoA hydratase or 3-hydroxyacyl-[acp]dehydratase, (v) an enoyl-[acp] reductase or a trans-2-enoyl-CoAreductase, and (vi) a pimeloyl-[acp]methyl ester methylesterase, thehost producing adipyl-[acp] or adipyl-CoA.

A recombinant host producing adipyl-[acp] or adipyl-CoA further caninclude at least one exogenous nucleic acid encoding one or more of athioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoatedehydrogenase, a 6-oxohexanoate dehydrogenase, a glutaconateCoA-transferase, a reversible succinyl-CoA ligase, an acetylatingaldehyde dehydrogenase, or a carboxylate reductase, the host producingadipate or adipate semialdehyde.

A recombinant host producing adipate semialdehyde further can include atleast one exogenous nucleic acid encoding a ω-transaminase, andproducing 6-aminohexanoate.

A recombinant host producing adipate semialdehyde further can include atleast one exogenous nucleic acid encoding a 4-hydroxybutyratedehydrogenase, a 5-hydroxypentanoate dehydrogenase or a6-hydroxyhexanoate dehydrogenase, the host producing 6-hydroxyhexanoicacid.

A recombinant host producing adipate semialdehyde, 6-aminohexanoate, or6-hydroxyhexanoic acid further can include a carboxylate reductase, aω-transaminase, a deacetylase, an N-acetyl transferase, or an alcoholdehydrogenase, the host producing hexamethylenediamine.

A recombinant host producing 6-hydroxyhexanoic acid further can includeat least one exogenous nucleic acid encoding a carboxylate reductase oran alcohol dehydrogenase, the host producing 1,6-hexanediol.

The recombinant host can be a prokaryote, e.g., from the genusEscherichia such as Escherichia coli; from the genus Clostridia such asClostridium ljungdahlii, Clostridium autoethanogenum or Clostridiumkluyveri; from the genus Corynebacteria such as Corynebacteriumglutamicum; from the genus Cupriavidus such as Cupriavidus necator orCupriavidus metallidurans; from the genus Pseudomonas such asPseudomonas fluorescens, Pseudomonas putida or Pseudomonas oleavorans;from the genus Delftia acidovorans, from the genus Bacillus such asBacillus subtillis; from the genes Lactobacillus such as Lactobacillusdelbrueckii; from the genus Lactococcus such as Lactococcus lactis orfrom the genus Rhodococcus such as Rhodococcus equi.

The recombinant host can be a eukaryote, e.g., a eukaryote from thegenus Aspergillus such as Aspergillus niger; from the genusSaccharomyces such as Saccharomyces cerevisiae; from the genus Pichiasuch as Pichia pastoris; from the genus Yarrowia such as Yarrowialipolytica, from the genus Issatchenkia such as Issathenkia orientalis,from the genus Debaryomyces such as Debaryomyces hansenii, from thegenus Arxula such as Arxula adenoinivorans, or from the genusKluyveromyces such as Kluyveromyces lactis.

Any of the recombinant hosts described herein further can include one ormore of the following attenuated enzymes: polyhydroxyalkanoate synthase,an acetyl-CoA thioesterase, a phosphotransacetylase forming acetate, anacetate kinase, a lactate dehydrogenase, a menaquinol-fumarateoxidoreductase, a 2-oxoacid decarboxylase producing isobutanol, analcohol dehydrogenase forming ethanol, a triose phosphate isomerase, apyruvate decarboxylase, a glucose-6-phosphate isomerase, atranshydrogenase dissipating the NADH or NADPH imbalance, an glutamatedehydrogenase dissipating the NADH or NADPH imbalance, aNADH/NADPH-utilizing glutamate dehydrogenase, a pimeloyl-CoAdehydrogenase; an acyl-CoA dehydrogenase accepting C6 building blocksand central precursors as substrates; a glutaryl-CoA dehydrogenase; or apimeloyl-CoA synthetase.

Any of the recombinant hosts described herein further can overexpressone or more genes encoding: an oxaloacetase, a PEP carboxylase, a PEPcarboxykinase, a pyruvate carboxylase, a PEP synthase, an acetyl-CoAsynthetase, a 6-phosphogluconate dehydrogenase; a transketolase; apuridine nucleotide transhydrogenase; a formate dehydrogenase; aglyceraldehyde-3P-dehydrogenase; a malic enzyme; a glucose-6-phosphatedehydrogenase; a fructose 1,6 diphosphatase; a L-alanine dehydrogenase;a L-glutamate dehydrogenase specific to the NADH or NADPH used togenerate a co-factor imbalance; a methanol dehydrogenase; a formaldehydedehydrogenase; a diamine transporter; a dicarboxylate transporter;S-adenosylmethionine synthetase; and/or a multidrug transporter.

The reactions of the pathways described herein can be performed in oneor more cell (e.g., host cell) strains (a) naturally expressing one ormore relevant enzymes, (b) genetically engineered to express one or morerelevant enzymes, or (c) naturally expressing one or more relevantenzymes and genetically engineered to express one or more relevantenzymes. Alternatively, relevant enzymes can be extracted from any ofthe above types of host cells and used in a purified or semi-purifiedform. Extracted enzymes can optionally be immobilized to a solidsubstrate such as the floors and/or walls of appropriate reactionvessels. Moreover, such extracts include lysates (e.g. cell lysates)that can be used as sources of relevant enzymes. In the methods providedby the document, all the steps can be performed in cells (e.g., hostcells), all the steps can be performed using extracted enzymes, or someof the steps can be performed in cells and others can be performed usingextracted enzymes.

Many of the enzymes described herein catalyze reversible reactions, andthe reaction of interest may be the reverse of the described reaction.The schematic pathways shown in FIGS. 1-6 illustrate the reaction ofinterest for each of the intermediates.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used to practicethe invention, suitable methods and materials are described below. Allpublications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including definitions, willcontrol. In addition, the materials, methods, and examples areillustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and the drawings, and from the claims. The word “comprising”in the claims may be replaced by “consisting essentially of” or with“consisting of,” according to standard practice in patent law.

DESCRIPTION OF DRAWINGS

FIG. 1A is a schematic of an exemplary biochemical pathway leading toadipyl-[acp] using NADPH-dependent enzymes and oxalyl-CoA andmalonyl-[acp] as central metabolites.

FIG. 1B is a schematic of an exemplary biochemical pathway leading toadipyl-CoA using NADPH-dependent enzymes and oxalyl-CoA and eitheracetyl-CoA or malonyl-CoA as central metabolites.

FIG. 1C is a schematic of an exemplary biochemical pathway leading toadipyl-CoA using NADH-dependent enzymes and oxalyl-CoA and eitheracetyl-CoA or malonyl-CoA as central metabolites.

FIG. 2 is a schematic of exemplary biochemical pathways leading toadipate using adipyl-[acp], adipyl-CoA, or adipate semialdehyde ascentral precursors.

FIG. 3 is a schematic of exemplary biochemical pathways leading to6-aminohexanoate or caprolactam using adipyl-CoA, adipate, or adipatesemialdehyde as central precursors.

FIG. 4 is a schematic of exemplary biochemical pathways leading tohexamethylenediamine using 6-aminohexanoate, 6-hydroxhexanoate oradipate semialdehyde as central precursors.

FIG. 5 is a schematic of exemplary biochemical pathways leading to6-hydroxhexanoate using adipate, adipyl-CoA, or adipate semialdehyde ascentral precursors.

FIG. 6 is a schematic of an exemplary biochemical pathway leading to1,6-hexanediol using 6-hydroxhexanoate as a central precursor.

FIGS. 7A-7G contain the amino acid sequences of an Escherichia colithioesterase encoded by tesB (see GenBank Accession No. AAA24665.1, SEQID NO: 1), an Escherichia coli thioesterase encoded by YciA (see GenBankAccession No. AAB60068.1, SEQ ID NO: 1), Mycobacterium marinumcarboxylate reductase (see Genbank Accession No. ACC40567.1, SEQ ID NO:3), a Mycobacterium smegmatis carboxylate reductase (see GenbankAccession No. ABK71854.1, SEQ ID NO: 4), a Segniliparus rugosuscarboxylate reductase (see Genbank Accession No. EFV11917.1, SEQ ID NO:5), a Mycobacterium massiliense carboxylate reductase (see GenbankAccession No. EIV11143.1, SEQ ID NO: 6), a Segniliparus rotunduscarboxylate reductase (see Genbank Accession No. ADG98140.1, SEQ ID NO:7), a Chromobacterium violaceum ω-transaminase (see Genbank AccessionNo. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas aeruginosa ω-transaminase(see Genbank Accession No. AAG08191.1, SEQ ID NO: 9), a Pseudomonassyringae ω-transaminase (see Genbank Accession No. AAY39893.1, SEQ IDNO: 10), a Rhodobacter sphaeroides ω-transaminase (see Genbank AccessionNo. ABA81135.1, SEQ ID NO: 11), an Escherichia coli ω-transaminase (seeGenbank Accession No. AAA57874.1, SEQ ID NO: 12), a Vibrio fluvialisω-transaminase (see Genbank Accession No. AEA39183.1, SEQ ID NO: 13), aBacillus subtilis phosphopantetheinyl transferase (see Genbank AccessionNo. CAA44858.1, SEQ ID NO:14), a Nocardia sp. NRRL 5646phosphopantetheinyl transferase (see Genbank Accession No. ABI83656.1,SEQ ID NO: 15), a Bacillus cereus malonyl-CoA methyltransferase (seeGenBank Accession No. AAS43086.1, SEQ ID NO:16), and an Escherichia colipimeloyl-[acp] methyl ester esterase (see GenBank Accession No.AAC76437.1, SEQ ID NO: 17).

FIG. 8 is a bar graph of the relative absorbance at 412 nm after 20minutes of released CoA as a measure of the activity of a thioesterasefor converting adipyl-CoA to adipate relative to the empty vectorcontrol.

FIG. 9 is a bar graph summarizing the change in absorbance at 340 nmafter 20 minutes, which is a measure of the consumption of NADPH andactivity of carboxylate reductases relative to the enzyme only controls(no substrate).

FIG. 10 is a bar graph of the change in absorbance at 340 nm after 20minutes, which is a measure of the consumption of NADPH and the activityof carboxylate reductases for converting adipate to adipate semialdehyderelative to the empty vector control.

FIG. 11 is a bar graph of the change in absorbance at 340 nm after 20minutes, which is a measure of the consumption of NADPH and the activityof carboxylate reductases for converting 6-hydroxhexanoate to6-hydroxhexanal relative to the empty vector control.

FIG. 12 is a bar graph of the change in absorbance at 340 nm after 20minutes, which is a measure of the consumption of NADPH and the activityof carboxylate reductases for converting N6-acetyl-6-aminohexanoate toN6-acetyl-6-aminohexanal relative to the empty vector control.

FIG. 13 is a bar graph of the change in absorbance at 340 nm after 20minutes, which is a measure of the consumption of NADPH and activity ofcarboxylate reductases for converting adipate semialdehyde to hexanedialrelative to the empty vector control.

FIG. 14 is a bar graph summarizing the percent conversion after 4 hoursof pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminaseactivity of the enzyme only controls (no substrate).

FIG. 15 is a bar graph of the percent conversion after 24 hours ofpyruvate to L-alanine (mol/mol) as a measure of the ω-transaminaseactivity for converting 6-aminohexanoate to adipate semialdehyderelative to the empty vector control.

FIG. 16 is a bar graph of the percent conversion after 4 hours ofL-alanine to pyruvate (mol/mol) as a measure of the ω-transaminaseactivity for converting adipate semialdehyde to 6-aminohexanoaterelative to the empty vector control.

FIG. 17 is a bar graph of the percent conversion after 4 hours ofpyruvate to L-alanine (mol/mol) as a measure of the ω-transaminaseactivity for converting hexamethylenediamine to 6-aminohexanal relativeto the empty vector control.

FIG. 18 is a bar graph of the percent conversion after 4 hours ofpyruvate to L-alanine (mol/mol) as a measure of the ω-transaminaseactivity for converting N6-acetyl-1,6-diaminohexane toN6-acetyl-6-aminohexanal relative to the empty vector control.

FIG. 19 is a bar graph of the percent conversion after 4 hours ofpyruvate to L-alanine (mol/mol) as a measure of the ω-transaminaseactivity for converting 6-aminohexanol to 6-oxohexanol relative to theempty vector control.

FIG. 20 is a table of the conversion after 1 hour of adipyl-CoA methylester to adipyl-CoA by pimeloyl-[acp] methyl ester methylesterase.

DETAILED DESCRIPTION

This document provides enzymes, non-natural pathways, cultivationstrategies, feedstocks, host microorganisms and attenuations to thehost's biochemical network, which generates a six carbon chain aliphaticbackbone from central metabolites in which one or two terminalfunctional groups may be formed leading to the synthesis of adipic acid,6-aminohexanoic acid, hexamethylenediamine, caprolactam, or1,6-hexanediol (referred to as “C6 building blocks” herein). As usedherein, the term “central precursor” is used to denote any metabolite inany metabolic pathway shown herein leading to the synthesis of a C6building block. The term “central metabolite” is used herein to denote ametabolite that is produced in all microorganisms to support growth.

Host microorganisms described herein can include endogenous pathwaysthat can be manipulated such that one or more C6 building blocks can beproduced. In an endogenous pathway, the host microorganism naturallyexpresses all of the enzymes catalyzing the reactions within thepathway. A host microorganism containing an engineered pathway does notnaturally express all of the enzymes catalyzing the reactions within thepathway but has been engineered such that all of the enzymes within thepathway are expressed in the host.

The term “exogenous” as used herein with reference to a nucleic acid (ora protein) and a host refers to a nucleic acid that does not occur in(and cannot be obtained from) a cell of that particular type as it isfound in nature or a protein encoded by such a nucleic acid. Thus, anon-naturally-occurring nucleic acid is considered to be exogenous to ahost once in the host. It is important to note thatnon-naturally-occurring nucleic acids can contain nucleic acidsubsequences or fragments of nucleic acid sequences that are found innature provided the nucleic acid as a whole does not exist in nature.For example, a nucleic acid molecule containing a genomic DNA sequencewithin an expression vector is non-naturally-occurring nucleic acid, andthus is exogenous to a host cell once introduced into the host, sincethat nucleic acid molecule as a whole (genomic DNA plus vector DNA) doesnot exist in nature. Thus, any vector, autonomously replicating plasmid,or virus (e.g., retrovirus, adenovirus, or herpes virus) that as a wholedoes not exist in nature is considered to be non-naturally-occurringnucleic acid. It follows that genomic DNA fragments produced by PCR orrestriction endonuclease treatment as well as cDNAs are considered to benon-naturally-occurring nucleic acid since they exist as separatemolecules not found in nature. It also follows that any nucleic acidcontaining a promoter sequence and polypeptide-encoding sequence (e.g.,cDNA or genomic DNA) in an arrangement not found in nature isnon-naturally-occurring nucleic acid. A nucleic acid that isnaturally-occurring can be exogenous to a particular host microorganism.For example, an entire chromosome isolated from a cell of yeast x is anexogenous nucleic acid with respect to a cell of yeast y once thatchromosome is introduced into a cell of yeast y.

In contrast, the term “endogenous” as used herein with reference to anucleic acid (e.g., a gene) (or a protein) and a host refers to anucleic acid (or protein) that does occur in (and can be obtained from)that particular host as it is found in nature. Moreover, a cell“endogenously expressing” a nucleic acid (or protein) expresses thatnucleic acid (or protein) as does a host of the same particular type asit is found in nature. Moreover, a host “endogenously producing” or that“endogenously produces” a nucleic acid, protein, or other compoundproduces that nucleic acid, protein, or compound as does a host of thesame particular type as it is found in nature.

For example, depending on the host and the compounds produced by thehost, one or more of the following enzymes may be expressed in the hostin addition to a malonyl-[acp] O-methyltransferase and a pimeloyl-[acp]methyl ester methylesterase: a β-ketoacyl-[acp] synthase, aβ-ketothiolase, a 3-oxoacyl-[acp] reductase, acetoacetyl-CoA reductase,a 3-hydroxyacyl-CoA dehydrogenase, a 3-hydroxybutyryl-CoA dehydrogenase,an enoyl-CoA hydratase, 3-hydroxyacyl-[acp] dehydratase, an enoyl-[acp]reductase, a trans-2-enoyl-CoA reductase, a thioesterase, a reversibleCoA ligase, a CoA-transferase, an acetylating aldehyde dehydrogenase, a6-oxohexanoate dehydrogenase, a 7-oxoheptanoate dehydrogenase, analdehyde dehydrogenase, a carboxylate reductase, a ω-transaminase, aN-acetyl transferase, an alcohol dehydrogenase, a deacetylase, a6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase,or a 4-hydroxybutyrate dehydrogenase. In recombinant hosts expressing acarboxylate reductase, a phosphopantetheinyl transferase also can beexpressed as it enhances activity of the carboxylate reductase.

For example, a recombinant host can include at least one exogenousnucleic acid encoding (i) a malonyl-[acp] O-methyltransferase, (ii) aβ-ketoacyl-[acp] synthase or a β-ketothiolase, (iii) a 3-oxoacyl-[acp]reductase, acetoacetyl-CoA reductase, a 3-hydroxyacyl-CoA dehydrogenaseor a 3-hydroxybutyryl-CoA dehydrogenase, (iv) an enoyl-CoA hydratase or3-hydroxyacyl-[acp] dehydratase, (v) an enoyl-[acp] reductase or atrans-2-enoyl-CoA reductase and (vi) a pimeloyl-[acp] methyl estermethylesterase, and produce adipyl-[acp] or adipyl-CoA.

Such recombinant hosts producing adipyl-[acp] or adipyl-CoA further caninclude at least one exogenous nucleic acid encoding one or more of athioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoatedehydrogenase, a 6-oxohexanoate dehydrogenase, a glutaconateCoA-transferase, a reversible succinyl-CoA ligase, an acetylatingaldehyde dehydrogenase, or a carboxylate reductase and produce adipicacid or adipate semialdehyde. For example, a recombinant host producingadipyl-[acp] or adipyl-CoA further can include a thioesterase, areversible Co-ligase (e.g., a reversible succinyl-CoA ligase), or a CoAtransferase (e.g., a glutaconate CoA-transferase) and produce adipicacid. For example, a recombinant host producing adipyl-CoA further caninclude an acetylating aldehyde dehydrogenase and produce adipatesemilaldehyde. For example, a recombinant host producing adipate furthercan include a carboxylate reductase and produce adipate semialdehyde.

A recombinant hosts producing adipate semialdehyde further can includeat least one exogenous nucleic acid encoding a ω-transaminase andproduce 6-aminohexanoate. In some embodiments, a recombinant hostproducing adipyl-CoA includes a carboxylate reductase and aω-transaminase to produce 6-aminohexanoate.

A recombinant host producing adipate or adipate semialdehyde further caninclude at least one exogenous nucleic acid encoding a6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase ora 4-hydroxybutyrate dehydrogenase, and produce 6-hydroxhexanoic acid. Insome embodiments, a recombinant host producing adipyl-CoA includes anacetylating aldehyde dehydrogenase, and a 6-hydroxyhexanoatedehydrogenase, a 5-hydroxypentanoate dehydrogenase or a4-hydroxybutyrate dehydrogenase to produce 6-hydroxhexanoate. In someembodiments, a recombinant host producing adipate includes a carboxylatereductase and a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoatedehydrogenase or a 4-hydroxybutyrate dehydrogenase to produce6-hydroxhexanoate.

A recombinant hosts producing 6-aminohexanoate, 6-hydroxhexanoate oradipate semialdehyde further can include at least one exogenous nucleicacid encoding a ω-transaminase, a deacetylase, a N-acetyl transferase,or an alcohol dehydrogenase, and produce hexamethylenediamine. Forexample, a recombinant host producing 6-hydroxhexanoate can include acarboxylate reductase with a phosphopantetheine transferase enhancer, aω-transaminase and an alcohol dehydrogenase.

A recombinant host producing 6-hydroxhexanoic acid further can includeone or more of a carboxylate reductase with a phosphopantetheinetransferase enhancer and an alcohol dehydrogenase, and produce1,6-hexanediol.

Within an engineered pathway, the enzymes can be from a single source,i.e., from one species or genus, or can be from multiple sources, i.e.,different species or genera. Nucleic acids encoding the enzymesdescribed herein have been identified from various organisms and arereadily available in publicly available databases such as GenBank orEMBL.

Any of the enzymes described herein that can be used for production ofone or more C6 building blocks can have at least 70% sequence identity(homology) (e.g., at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or100%) to the amino acid sequence of the corresponding wild-type enzyme.It will be appreciated that the sequence identity can be determined onthe basis of the mature enzyme (e.g., with any signal sequence removed).

For example, a thioesterase described herein can have at least 70%sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 95%,97%, 98%, 99%, or 100%) to the amino acid sequence of an Escherichiacoli thioesterase encoded by tesB (see GenBank Accession No. AAA24665.1,SEQ ID NO: 1) or an Escherichia coli thioesterase encoded by YciA (seeGenBank Accession No. AAB60068.1, SEQ ID NO: 2). See FIG. 7A.

For example, a carboxylate reductase described herein can have at least70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%,95%, 97%, 98%, 99%, or 100%) to the amino acid sequence of aMycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO:3), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQID NO: 4), a Segniliparus rugosus (see Genbank Accession No. EFV11917.1,SEQ ID NO: 5), a Mycobacterium massiliense (see Genbank Accession No.EIV11143.1, SEQ ID NO: 6), or a Segniliparus rotundus (see GenbankAccession No. ADG98140.1, SEQ ID NO: 7) carboxylate reductase. See,FIGS. 7A-7E.

For example, a ω-transaminase described herein can have at least 70%sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 95%,97%, 98%, 99%, or 100%) to the amino acid sequence of a Chromobacteriumviolaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), aPseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO:9), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ IDNO: 10), a Rhodobacter sphaeroides (see Genbank Accession No.ABA81135.1, SEQ ID NO: 11), an Escherichia coli (see Genbank AccessionNo. AAA57874.1, SEQ ID NO: 12), or a Vibrio fluvialis (see GenbankAccession No. AEA39183.1, SEQ ID NO: 13) ω-transaminase. Some of theseCD-transaminases are diamine ω-transaminases. See, FIGS. 7E-7F.

For example, a phosphopantetheinyl transferase described herein can haveat least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%,90%, 95%, 97%, 98%, 99%, or 100%) to the amino acid sequence of aBacillus subtilis phosphopantetheinyl transferase (see Genbank AccessionNo. CAA44858.1, SEQ ID NO:14) or a Nocardia sp. NRRL 5646phosphopantetheinyl transferase (see Genbank Accession No. ABI83656.1,SEQ ID NO:15). See FIGS. 7F and 7G.

For example, a malonyl-CoA methyltransferase described herein can haveat least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%,90%, 95%, 97%, 98%, 99%, or 100%) to the amino acid sequence of aBacillus cereus malonyl-CoA methyltransferase (see GenBank Accession No.AAS43086.1, SEQ ID NO:16). See, FIG. 7G.

For example, a pimeloyl-[acp] methyl ester esterase described herein canhave at least 70% sequence identity (homology) (e.g., at least 75%, 80%,85%, 90%, 95%, 97%, 98%, 99%, or 100%) to the amino acid sequence of anEscherichia coli pimeloyl-[acp] methyl ester esterase (see GenBankAccession No. AAC76437.1, SEQ ID NO:17). See, FIG. 7G.

The percent identity (homology) between two amino acid sequences can bedetermined as follows. First, the amino acid sequences are aligned usingthe BLAST 2 Sequences (Bl2seq) program from the stand-alone version ofBLASTZ containing BLASTP version 2.0.14. This stand-alone version ofBLASTZ can be obtained from Fish & Richardson's web site (e.g.,www.fr.com/blast/) or the U.S. government's National Center forBiotechnology Information web site (www.ncbi.nlm.nih.gov). Instructionsexplaining how to use the Bl2seq program can be found in the readme fileaccompanying BLASTZ. Bl2seq performs a comparison between two amino acidsequences using the BLASTP algorithm. To compare two amino acidsequences, the options of Bl2seq are set as follows: -i is set to a filecontaining the first amino acid sequence to be compared (e.g.,C:\seq1.txt); -j is set to a file containing the second amino acidsequence to be compared (e.g., C:\seq2.txt); -p is set to blastp; -o isset to any desired file name (e.g., C:\output.txt); and all otheroptions are left at their default setting. For example, the followingcommand can be used to generate an output file containing a comparisonbetween two amino acid sequences: C:\Bl2seq -i c:\seq1.txt -jc:\seq2.txt -p blastp -o c:\output.txt. If the two compared sequencesshare homology (identity), then the designated output file will presentthose regions of homology as aligned sequences. If the two comparedsequences do not share homology (identity), then the designated outputfile will not present aligned sequences. Similar procedures can befollowing for nucleic acid sequences except that blastn is used.

Once aligned, the number of matches is determined by counting the numberof positions where an identical amino acid residue is presented in bothsequences. The percent identity (homology) is determined by dividing thenumber of matches by the length of the full-length polypeptide aminoacid sequence followed by multiplying the resulting value by 100. It isnoted that the percent identity (homology) value is rounded to thenearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 is roundeddown to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 is rounded upto 78.2. It also is noted that the length value will always be aninteger.

It will be appreciated that a number of nucleic acids can encode apolypeptide having a particular amino acid sequence. The degeneracy ofthe genetic code is well known to the art; i.e., for many amino acids,there is more than one nucleotide triplet that serves as the codon forthe amino acid. For example, codons in the coding sequence for a givenenzyme can be modified such that optimal expression in a particularspecies (e.g., bacteria or fungus) is obtained, using appropriate codonbias tables for that species.

Functional fragments of any of the enzymes described herein can also beused in the methods of the document. The term “functional fragment” asused herein refers to a peptide fragment of a protein that has at least25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 95%;98%; 99%; 100%; or even greater than 100%) of the activity of thecorresponding mature, full-length, wild-type protein. The functionalfragment can generally, but not always, be comprised of a continuousregion of the protein, wherein the region has functional activity.

This document also provides (i) functional variants of the enzymes usedin the methods of the document and (ii) functional variants of thefunctional fragments described above. Functional variants of the enzymesand functional fragments can contain additions, deletions, orsubstitutions relative to the corresponding wild-type sequences. Enzymeswith substitutions will generally have not more than 50 (e.g., not morethan one, two, three, four, five, six, seven, eight, nine, ten, 12, 15,20, 25, 30, 35, 40, or 50) amino acid substitutions (e.g., conservativesubstitutions). This applies to any of the enzymes described herein andfunctional fragments. A conservative substitution is a substitution ofone amino acid for another with similar characteristics. Conservativesubstitutions include substitutions within the following groups: valine,alanine and glycine; leucine, valine, and isoleucine; aspartic acid andglutamic acid; asparagine and glutamine; serine, cysteine, andthreonine; lysine and arginine; and phenylalanine and tyrosine. Thenonpolar hydrophobic amino acids include alanine, leucine, isoleucine,valine, proline, phenylalanine, tryptophan and methionine. The polarneutral amino acids include glycine, serine, threonine, cysteine,tyrosine, asparagine and glutamine. The positively charged (basic) aminoacids include arginine, lysine and histidine. The negatively charged(acidic) amino acids include aspartic acid and glutamic acid. Anysubstitution of one member of the above-mentioned polar, basic or acidicgroups by another member of the same group can be deemed a conservativesubstitution. By contrast, a nonconservative substitution is asubstitution of one amino acid for another with dissimilarcharacteristics.

Deletion variants can lack one, two, three, four, five, six, seven,eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acidsegments (of two or more amino acids) or non-contiguous single aminoacids. Additions (addition variants) include fusion proteins containing:(a) any of the enzymes described herein or a fragment thereof; and (b)internal or terminal (C or N) irrelevant or heterologous amino acidsequences. In the context of such fusion proteins, the term“heterologous amino acid sequences” refers to an amino acid sequenceother than (a). A heterologous sequence can be, for example a sequenceused for purification of the recombinant protein (e.g., FLAG,polyhistidine (e.g., hexahistidine), hemagglutinin (HA),glutathione-S-transferase (GST), or maltosebinding protein (MBP)).Heterologous sequences also can be proteins useful as detectablemarkers, for example, luciferase, green fluorescent protein (GFP), orchloramphenicol acetyl transferase (CAT). In some embodiments, thefusion protein contains a signal sequence from another protein. Incertain host cells (e.g., yeast host cells), expression and/or secretionof the target protein can be increased through use of a heterologoussignal sequence. In some embodiments, the fusion protein can contain acarrier (e.g., KLH) useful, e.g., in eliciting an immune response forantibody generation) or ER or Golgi apparatus retention signals.Heterologous sequences can be of varying length and in some cases can bea longer sequences than the full-length target proteins to which theheterologous sequences are attached.

Engineered hosts can naturally express none or some (e.g., one or more,two or more, three or more, four or more, five or more, or six or more)of the enzymes of the pathways described herein. Thus, a pathway withinan engineered host can include all exogenous enzymes, or can includeboth endogenous and exogenous enzymes. Endogenous genes of theengineered hosts also can be disrupted to prevent the formation ofundesirable metabolites or prevent the loss of intermediates in thepathway through other enzymes acting on such intermediates. Engineeredhosts can be referred to as recombinant hosts or recombinant host cells.As described herein recombinant hosts can include nucleic acids encodingone or more of a methyltransferase, a synthase, β-ketothiolase, adehydratase, a hydratase, a dehydrogenase, a methylesterase, athioesterase, a reversible CoA-ligase, a CoA-transferase, a reductase,deacetylase, N-acetyl transferase or a ω-transaminase as described inmore detail below.

In addition, the production of one or more C6 building blocks can beperformed in vitro using the isolated enzymes described herein, using alysate (e.g., a cell lysate) from a host microorganism as a source ofthe enzymes, or using a plurality of lysates from different hostmicroorganisms as the source of the enzymes.

Enzymes Generating the C6 Aliphatic Backbone for Conversion to C6Building Blocks

As depicted in FIG. 1A, FIG. 1B and FIG. 1C, the C6 aliphatic backbonefor conversion to one or more C6 building blocks can be formed frommalonyl-[acp], or acetyl-CoA and malonyl-CoA, via two cycles of methylester shielded carbon chain elongation associated with biotinbiosynthesis using either NADH or NADPH dependent enzymes.

In some embodiments, a methyl ester shielded carbon chain elongationroute comprises using a malonyl-[acp] O-methyltransferase to form anoxalyl-CoA methyl ester, and then performing two cycles of carbon chainelongation using malonyl-[acp] and a β-ketoacyl-[acp] synthase, a3-oxoacyl-[acp] reductase, a 3-hydroxyacyl-[acp] dehydratase, and anenoyl-[acp] reductase. A pimeloyl-[acp] methyl ester esterase can beused to cleave the resulting adipyl-[acp] methyl ester.

In some embodiments, a methyl ester shielded carbon chain elongationroute comprises using a malonyl-[acp] O-methyltransferase to form anoxalyl-CoA methyl ester, and then performing two cycles of carbon chainelongation using either acetyl-CoA or malonyl-CoA and (i) aβ-ketothiolase or a β-ketoacyl-[acp] synthase, (ii) an acetoacetyl-CoAreductase, a 3-oxoacyl-[acp] reductase, or a 3-hydroxybutyryl-CoAdehydrogenase, (iii) enoyl-CoA hydratase, and (iv) a trans-2-enoyl-CoAreductase. A pimeloyl-[acp] methyl ester esterase can be used to cleavethe resulting adipyl-CoA methyl ester.

In some embodiments, a methyltransferase can be a malonyl-[acp]O-methyltransferase classified, for example, under EC 2.1.1.197 such asthe gene product of bioC from Bacillus cereus (see Genbank Accession No.AAS43086.1, SEQ ID NO:16) (see, for example, Lin, 2012, Biotin Synthesisin Escherichia coli, Ph.D. Dissertation, University of Illinois atUrbana-Champaign).

In some embodiments, a β-ketothiolase may be classified, for example,under EC 2.3.1.16, such as the gene product of bktB. The β-ketothiolaseencoded by bktB from Cupriavidus necator accepts acetyl-CoA andbutanoyl-CoA as substrates, forming the CoA-activated C6 aliphaticbackbone (see, e.g., Haywood et al., FEMS Microbiology Letters, 1988,52:91-96; Slater et al., J. Bacteriol., 1998, 180(8):1979-1987).

In some embodiments, a β-ketoacyl-[acp] synthase may be classified, forexample, under EC 2.3.1.—(e.g., EC 2.3.1.41, EC 2.3.1.179 or EC2.3.1.180) such as the gene product of fabB, fabF, or fabH.

In some embodiments, a 3-hydroxyacyl-CoA dehydrogenase may be classifiedunder EC 1.1.1.35, such as the gene product of fadB, or classified underEC 1.1.1.157, such as the gene product of hbd (can be referred to as a3-hydroxybutyryl-CoA dehydrogenase), or classified under EC 1.1.1.36,such as the gene product of phaB (see, for example, Liu & Chen, Appl.Microbiol. Biotechnol., 2007, 76(5), 1153-1159; Shen et al., Appl.Environ. Microbiol., 2011, 77(9), 2905-2915; or Budde et al., J.Bacteriol., 2010, 192(20), 5319-5328).

In some embodiments, a 3-oxoacyl-CoA reductase may be classified underEC 1.1.1.100, such as the gene product of fabG (Budde et al., 2010,supra; Nomura et al., Appl. Environ. Microbiol., 2005, 71(8),4297-4306).

In some embodiments, an enoyl-CoA hydratase may be classified under EC4.2.1.17, such as the gene product of crt, or classified under EC4.2.1.119, such as the gene product of phaJ (Shen et al., 2011, supra;or Fukui et al., J. Bacteriol., 1998, 180(3), 667-673).

In some embodiments, an enoyl-[acp] dehydratase such as a3-hydroxyacyl-[acp] dehydratase may be classified under EC 4.2.1.59,such as the gene product of fabZ.

In some embodiments, a trans-2-enoyl-CoA reductase may be classifiedunder EC 1.3.1.—(e.g., EC 1.3.1.38, EC 1.3.1.8, EC 1.3.1.44), such asthe gene product of ter (Nishimaki et al., J. Biochem., 1984, 95,1315-1321; Shen et al., 2011, supra) or tdter (Bond-Watts et al.,Biochemistry, 2012, 51, 6827-6837).

In some embodiments, an enoyl-[acp] reductase may be classified under EC1.3.1.10 such as the gene product of fabI.

In some embodiments, a pimeloyl-[acp] methyl ester esterase may beclassified, for example, under EC 3.1.1.85 such as the gene product ofbioH from E. coli. See Genbank Accession No. AAC76437.1, SEQ ID NO:17.

Enzymes Generating the Terminal Carboxyl Groups in the Biosynthesis ofC6 Building Blocks

As depicted in FIG. 2, a terminal carboxyl group can be enzymaticallyformed using a thioesterase, an aldehyde dehydrogenase, a7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, aCoA-transferase or a reversible CoA-ligase.

In some embodiments, the second terminal carboxyl group leading to thesynthesis of a C6 building block is enzymatically formed by athioesterase classified, for example, under EC 3.1.2.—, such as the geneproduct of YciA, tesB (GenBank Accession No. AAB60068.1, SEQ ID NO: 2;Genbank Accession No. AAA24665.1, SEQ ID NO: 1) or Acot13 (see, forexample, Cantu et al., Protein Science, 2010, 19, 1281-1295; Zhuang etal., Biochemistry, 2008, 47(9), 2789-2796; or Naggert et al., J. Biol.Chem., 1991, 266(17), 11044-11050).

In some embodiments, the second terminal carboxyl group leading to thesynthesis of a C6 building block is enzymatically formed by anacyl-[acp] thioesterase classified under EC 3.1.2.—, such as the geneproduct of fatB or tesA. The acyl-[acp] thioesterases encoded by GenbankAccession Nos. ABJ63754.1 and CCC78182.1 have C6-C8 chain lengthspecificity (Jing et al, 2011, BMC Biochemistry, 12(44)).

In some embodiments, the second terminal carboxyl group leading to thesynthesis of adipic acid is enzymatically formed by an aldehydedehydrogenase classified, for example, under EC 1.2.1.3 (see, forexample, Guerrillot & Vandecasteele, Eur. J. Biochem., 1977, 81,185-192).

In some embodiments, the second terminal carboxyl group leading to thesynthesis of adipic acid is enzymatically formed by a dehydrogenaseclassified under EC 1.2.1.—such as a 6-oxohexanoate dehydrogenase (e.g.,the gene product of ChnE from Acinetobacter sp.) or a 7-oxoheptanoatedehydrogenase (e.g., such as the gene product of ThnG from Sphingomonasmacrogolitabida). See, for example, Iwaki et al., Appl. Environ.Microbiol., 1999, 65(11), 5158-5162; or Lopez-Sanchez et al., Appl.Environ. Microbiol., 2010, 76(1), 110-118. For example, a 6-oxohexanoatedehydrogenase can be classified under EC 1.2.1.63. For example, a7-oxoheptanoate dehydrogenase can be classified under EC 1.2.1.—.

In some embodiments, the second terminal carboxyl group leading to thesynthesis of adipic acid is enzymatically formed by a CoA-transferase(e.g., a glutaconate CoA-transferase) classified, for example, under EC2.8.3.12 such as from Acidaminococcus fermentans. See, for example,Buckel et al., 1981, Eur. J. Biochem., 118:315-321.

In some embodiments, the second terminal carboxyl group leading to thesynthesis of adipic acid is enzymatically formed by a reversibleCoA-ligase (e.g., a succinate-CoA ligase) classified, for example, underEC 6.2.1.5 such as from Thermococcus kodakaraensis. See, for example,Shikata et al., 2007, J. Biol. Chem., 282(37):26963-26970.

Enzymes Generating the Terminal Amine Groups in the Biosynthesis of C6Building Blocks

As depicted in FIG. 3 and FIG. 4, terminal amine groups can beenzymatically formed using a ω-transaminase or a deacetylase.

In some embodiments, the first or second terminal amine group leading tothe synthesis of 6-aminohexanoic acid is enzymatically formed by aω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19,EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as that obtained fromChromobacterium violaceum (Genbank Accession No. AAQ59697.1, SEQ ID NO:8), Pseudomonas aeruginosa (Genbank Accession No. AAG08191.1, SEQ ID NO:9), Pseudomonas syringae (Genbank Accession No. AAY39893.1, SEQ ID NO:10), Rhodobacter sphaeroides (Genbank Accession No. ABA81135.1, SEQ IDNO: 11), Escherichia coli (Genbank Accession No. AAA57874.1, SEQ ID NO:12), Vibrio Fluvialis (Genbank Accession No. AAA57874.1, SEQ ID NO: 13),Streptomyces griseus, or Clostridium viride. Some of theseω-transaminases are diamine ω-transaminases (e.g., SEQ ID NO:12). Forexample, the ω-transaminases classified, for example, under EC 2.6.1.29or EC 2.6.1.82 may be diamine ω-transaminases.

The reversible ω-transaminase from Chromobacterium violaceum (GenbankAccession No. AAQ59697.1, SEQ ID NO: 8) has demonstrated analogousactivity accepting 6-aminohexanoic acid as amino donor, thus forming thefirst terminal amine group in adipate semialdehyde (Kaulmann et al.,Enzyme and Microbial Technology, 2007, 41, 628-637).

The reversible 4-aminobubyrate:2-oxoglutarate transaminase fromStreptomyces griseus has demonstrated analogous activity for theconversion of 6-aminohexanoate to adipate semialdehyde (Yonaha et al.,Eur. J. Biochem., 1985, 146:101-106).

The reversible 5-aminovalerate transaminase from Clostridium viride hasdemonstrated analogous activity for the conversion of 6-aminohexanoateto adipate semialdehyde (Barker et al., J. Biol. Chem., 1987, 262(19),8994-9003).

In some embodiments, a terminal amine group leading to the synthesis of6-aminohexanoate or hexamethylenediamine is enzymatically formed by adiamine ω-transaminase. For example, the second terminal amino group canbe enzymatically formed by a diamine ω-transaminase classified, forexample, under EC 2.6.1.29 or classified, for example, under EC2.6.1.82, such as the gene product of YgjG from E. coli (GenbankAccession No. AAA57874.1, SEQ ID NO: 12).

The gene product of ygjG accepts a broad range of diamine carbon chainlength substrates, such as putrescine, cadaverine and spermidine (see,for example, Samsonova et al., BMC Microbiology, 2003, 3:2).

The diamine ω-transaminase from E. coli strain B has demonstratedactivity for 1,7 diaminoheptane (Kim, The Journal of Chemistry, 1964,239(3), 783-786).

In some embodiments, the second terminal amine group leading to thesynthesis of hexamethylenediamine is enzymatically formed by adeacetylase such as acetylputrescine deacetylase classified, forexample, under EC 3.5.1.62. The acetylputrescine deacetylase fromMicrococcus luteus K-11 accepts a broad range of carbon chain lengthsubstrates, such as acetylputrescine, acetylcadaverine andN⁸-acetylspermidine (see, for example, Suzuki et al., 1986, BBA—GeneralSubjects, 882(1):140-142).

Enzymes Generating the Terminal Hydroxyl Groups in the Biosynthesis ofC6 Building Blocks

As depicted in FIG. 5 and FIG. 6, a terminal hydroxyl group can beenzymatically formed using an alcohol dehydrogenase.

In some embodiments, a terminal hydroxyl group leading to the synthesisof 1,6 hexanediol is enzymatically formed by an alcohol dehydrogenaseclassified, for example, under EC 1.1.1.—(e.g., 1, 2, 21, or 184) suchas the gene product of YMR318C (classified, for example, under EC1.1.1.2, see Genbank Accession No. CAA90836.1) (Larroy et al., 2002,Biochem J., 361(Pt 1), 163-172), the gene product of the gene product ofYghD, the gene product of cpnD (Iwaki et al., 2002, Appl. Environ.Microbiol., 68(11):5671-5684), the gene product of gabD (Lütke-Eversloh& Steinbüchel, 1999, FEMS Microbiology Letters, 181(1):63-71), or a6-hydroxyhexanoate dehydrogenase classified, for example, under EC1.1.1.258 such as the gene product of ChnD (Iwaki et al., Appl. Environ.Microbiol., 1999, supra).

Biochemical Pathways

Pathways Using NADPH-Specific Enzymes to Adipyl-[acp] as CentralPrecursor Leading to C6 Building Blocks

In some embodiments, adipyl-[acp] is synthesized from the centralmetabolite oxalyl-CoA, by conversion of oxalyl-CoA to oxalyl-CoA methylester by a malonyl-CoA O-methyltransferase classified, for example,under EC 2.1.1.197 such as the gene product of bioC; followed byconversion with malonyl-[acp] to 3-oxosuccinyl-[acp] methyl ester by aβ-ketoacyl-[acp] synthase classified, for example, under EC2.3.1.—(e.g., EC 2.3.1.41, EC 2.3.1.179 or EC 2.3.1.180) such as thegene product of fabB, fabF or fabH; followed by conversion to3-hydroxy-succinyl-[acp] methyl ester by a 3-oxoacyl-[acp] reductaseclassified, for example, under EC 1.1.1.100 such as the gene product offabG; followed by conversion to 2,3-dehydrosuccinyl-[acp] methyl esterby a 3-hydroxyacyl-[acp] dehydratase classified, for example, under EC4.2.1.59 such as the gene product of fabZ; followed by conversion tosuccinyl-[acp] methyl ester by an enoyl-[acp] reductase classified, forexample, under EC 1.3.1.10 such as the gene product of fabI; followed byconversion to 3-oxoadipyl-[acp] methyl ester by a β-ketoacyl-[acp]synthase classified, for example, under EC 2.3.1.—(e.g., EC 2.3.1.41 orEC 2.3.1.179) such as the gene product of fabB or fabF; followed byconversion to 3-hydroxy-adipyl-[acp] methyl ester by a 3-oxoacyl-[acp]reductase classified, for example, under EC 1.1.1.100 such as the geneproduct of fabG; followed by conversion to 2,3-dehydroadipyl-[acp]methyl ester by a 3-hydroxyacyl-[acp] dehydratase classified, forexample, under EC 4.2.1.59 such as the gene product of fabZ; followed byconversion to adipyl-[acp] methyl ester by an enoyl-[acp] reductaseclassified, for example, under EC 1.3.1.10 such as the gene product offabI; followed by conversion to adipyl-[acp] by a pimeloyl-[acp] methylester esterase classified, for example, under EC 3.1.1.85 such as thegene product of bioH. See FIG. 1A.

Pathways Using NADPH-Specific Enzymes to Adipyl-CoA as Central PrecursorLeading to C6 Building Blocks

In some embodiments, adipyl-CoA is synthesized from the centralmetabolite oxalyl-CoA, by conversion of oxalyl-CoA to oxalyl-CoA methylester by a malonyl-CoA O-methyltransferase classified, for example,under EC 2.1.1.197 such as the gene product of bioC; followed byconversion with acetyl-CoA to 3-oxosuccinyl-CoA methyl ester by aβ-ketothiolase classified, for example, under EC 2.3.1.16 such as thegene product of bktB or by conversion with malonyl-CoA by aβ-ketoacyl-[acp] synthase classified, for example, under EC 2.3.1.180such as the gene product of fabH; followed by conversion to3-hydroxy-succinyl-CoA methyl ester by a 3-oxoacyl-[acp] reductaseclassified, for example, under EC 1.1.1.100 such as the gene product offabG or an acetoacetyl-CoA reductase classified, for example, under EC1.1.1.36 such as the gene product of phaB; followed by conversion to2,3-dehydrosuccinyl-CoA methyl ester by an enoyl-CoA hydrataseclassified, for example, under EC 4.2.1.119 such as the gene product ofphaJ; followed by conversion to succinyl-CoA methyl ester by a reductaseclassified, for example, under EC 1.3.1.—such as an enoyl-[acp]reductase (classified under EC 1.3.1.10) such as the gene product offabI or a trans-2-enoyl-CoA reductase (classified under EC 1.3.1.38, EC1.3.1.8, or EC 1.3.1.44) such as the gene product of ter or tdter;followed by conversion to 3-oxoadipyl-CoA methyl ester by aβ-ketoacyl-[acp] synthase classified, for example, under EC2.3.1.—(e.g., EC 2.3.1.41 or EC 2.3.1.179) such as the gene product offabB or fabF, or a β-ketothiolase classified, for example, under EC2.3.1.16 such as the gene product of bktB; followed by conversion to3-hydroxy-adipyl-CoA methyl ester by a 3-oxoacyl-[acp] reductaseclassified, for example, under EC 1.1.1.100 such as the gene product offabG or an acetoacetyl-CoA reductase classified, for example, under EC1.1.1.36 such as the gene product of phaB; followed by conversion to2,3-dehydroadipyl-CoA methyl ester by an enoyl-CoA hydratase classified,for example, under EC 4.2.1.119 such as the gene product of phaJ;followed by conversion to adipyl-CoA methyl ester by a reductaseclassified, for example, under EC 1.3.1.—such as an enoyl-[acp]reductase (EC 1.3.1.10) such as the gene product of fabI or atrans-2-enoyl-CoA reductase (EC 1.3.1.38, EC 1.3.1.8, or EC 1.3.1.44)such as the gene product of ter or tdter; followed by conversion toadipyl-CoA by a pimeloyl-[acp] methyl ester esterase classified, forexample, under EC 3.1.1.85 such as the gene product of bioH. See FIG.1B.

Pathways Using NADH-Specific Enzymes to Adipyl-CoA as Central PrecursorLeading to C6 Building Blocks

In some embodiments, adipyl-CoA is synthesized from the centralmetabolite, oxalyl-CoA, by conversion of oxalyl-CoA to oxalyl-CoA methylester by a malonyl-CoA O-methyltransferase classified, for example,under EC 2.1.1.197 such as the gene product of bioC; followed byconversion with acetyl-CoA to 3-oxosuccinyl-CoA methyl ester by aβ-ketothiolase classified, for example, under EC 2.3.1.16 such as thegene product of bktB or by conversion with malonyl-CoA by aβ-ketoacyl-[acp] synthase classified, for example, under EC 2.3.1.180such as the gene product of fabH; followed by conversion to3-hydroxy-succinyl-CoA methyl ester by a 3-hydroxyacyl-CoA dehydrogenaseclassified, for example, under EC 1.1.1.—(e.g., EC 1.1.1.35 or EC1.1.1.157) such as the gene product of fadB or hbd; followed byconversion to 2,3-dehydrosuccinyl-CoA methyl ester by an enoyl-CoAhydratase classified, for example, under EC 4.2.1.17 such as the geneproduct of crt; followed by conversion to succinyl-CoA methyl ester by atrans-2-enoyl-CoA reductase classified, for example, under EC 1.3.1.44such as the gene product of ter or tdter; followed by conversion to3-oxoadipyl-CoA methyl ester by a β-ketoacyl-[acp] synthase classified,for example, under EC 2.3.1.—(e.g., EC 2.3.1.41 or EC 2.3.1.179) such asthe gene product of fabB or fabF or a β-ketothiolase classified, forexample, under EC 2.3.1.16 such as the gene product of bktB; followed byconversion to 3-hydroxy-adipyl-CoA methyl ester by a 3-hydroxyacyl-CoAdehydrogenase classified, for example, under EC 1.1.1.35 such as thegene product of fadB or under EC 1.1.1.157 such as the gene product ofhbd; followed by conversion to 2,3-dehydroadipyl-CoA methyl ester by anenoyl-CoA hydratase classified, for example, under EC 4.2.1.17 such asthe gene product of crt; followed by conversion to adipyl-CoA methylester by a trans-2-enoyl-CoA reductase classified, for example, under EC1.3.1.44 such as the gene product of ter or tdter; followed byconversion to adipyl-CoA by a pimeloyl-[acp] methyl ester esteraseclassified under EC 3.1.1.85 such as the gene product of bioH. See FIG.1C.

Pathways Using Adipyl-CoA or Adipyl-[acp] as Central Precursors toAdipate

In some embodiments, adipic acid is synthesized from the centralprecursor, adipyl-CoA, by conversion of adipyl-CoA to adipatesemialdehyde by an acetylating aldehyde dehydrogenase classified, forexample, under EC 1.2.1.10 such as the gene product of PduB or PduP(see, for example, Lan et al., 2013, Energy Environ. Sci., 6:2672-2681);followed by conversion to adipic acid by a 7-oxoheptanoate dehydrogenaseclassified, for example, under EC 1.2.1.—such as the gene product ofThnG, a 6-oxohexanoate dehydrogenase classified, for example, under EC1.2.1.—such as the gene product of ChnE, or an aldehyde dehydrogenaseclassified, for example, under C 1.2.1.3. See FIG. 2.

In some embodiments, adipic acid is synthesized from the centralprecursor, adipyl-CoA, by conversion of adipyl-CoA to adipate by athioesterase classified, for example, under EC 3.1.2.—such as the geneproducts of YciA, tesB (GenBank Accession No. AAB60068.1, SEQ ID NO: 2;Genbank Accession No. AAA24665.1, SEQ ID NO: 1) or Acot13. See FIG. 2.

In some embodiments, adipic acid is synthesized from the centralprecursor, adipyl-[acp], by conversion of adipyl-[acp] to adipate by athioesterase classified, for example, under EC 3.1.2.—such as the geneproducts encoded by Genbank Accession No. ABJ63754.1, Genbank AccessionNo. CCC78182.1, tesA or fatB. See FIG. 2.

In some embodiments, adipate is synthesized from the central precursor,adipyl-CoA, by conversion of adipyl-CoA to adipate by a CoA-transferasesuch as a glutaconate CoA-transferase classified, for example, under EC2.8.3.12. See FIG. 2.

In some embodiments, adipate is synthesized from the central precursor,adipyl-CoA, by conversion of adipyl-CoA to adipate by a reversibleCoA-ligase such as a reversible succinate-CoA ligase classified, forexample, under EC 6.2.1.5. See FIG. 2.

In some embodiments, adipate is synthesized from the central precursor,adipate semialdehyde, by conversion of adipate semialdehyde to adipateby a 6-oxohexanoate dehydrogenase or a 7-oxoheptanoate dehydrogenase(classified, for example, under EC 1.2.1.—) such as the gene product ofThnG or ChnE, or an aldehyde dehydrogenase classified, for example,under EC 1.2.1.3. See FIG. 2.

Pathways Using Adipyl-CoA, Adipate Semialdehyde, or ε-Caprolactam asCentral Precursor to 6-Aminohexanoate

In some embodiments, 6-aminohexanoate is synthesized from the centralprecursor, adipyl-CoA, by conversion of adipyl-CoA to adipatesemialdehyde by an acetylating aldehyde dehydrogenase classified, forexample, EC 1.2.1.10, such as the gene product of PduB or PduP; followedby conversion of adipate semialdehyde to 6-aminohexanoate by aω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19,EC 2.6.1.29, EC 2.6.1.48 or EC 2.6.1.82. See FIG. 3.

In some embodiments, 6-aminohexanoate is synthesized from the centralprecursor, adipate semialdehyde, by conversion of adipate semialdehydeto 6-aminohexanoate by a ω-transaminase (e.g., EC 2.6.1.18, EC 2.6.1.19,or EC 2.6.1.48). See FIG. 3.

In some embodiments, 6-aminohexanoate is synthesized from the centralprecursor, adipate, by conversion of adipate to adipate semialdehyde bya carboxylate reductase classified, for example, under EC 1.2.99.6 suchas the gene product of car in combination with a phosphopantetheinetransferase enhancer (e.g., encoded by a sfp (Genbank Accession No.CAA44858.1, SEQ ID NO:14) gene from Bacillus subtilis or npt (GenbankAccession No. ABI83656.1, SEQ ID NO:15) gene from Nocardia) or the geneproducts of GriC and GriD from Streptomyces griseus (Suzuki et al., J.Antibiot., 2007, 60(6), 380-387); followed by conversion of adipatesemialdehyde to 6-aminohexanoate by a ω-transaminase (e.g., EC 2.6.1.18,EC 2.6.1.19, EC 2.6.1.48, EC 2.6.1.29, EC 2.6.1.82 such as SEQ IDNOs:8-13). The carboxylate reductase can be obtained, for example, fromMycobacterium marinum (Genbank Accession No. ACC40567.1, SEQ ID NO: 3),Mycobacterium smegmatis (Genbank Accession No. ABK71854.1, SEQ ID NO:4), Segniliparus rugosus (Genbank Accession No. EFV11917.1, SEQ ID NO:5), Mycobacterium massiliense (Genbank Accession No. EIV11143.1, SEQ IDNO: 6), or Segniliparus rotundus (Genbank Accession No. ADG98140.1, SEQID NO: 7). See FIG. 3.

In some embodiments, ε-caprolactam is synthesized from 6-aminohexanoateby a hydrolase classified, for example, under EC 3.5.2.—. See FIG. 3.

Pathway Using 6-Aminohexanoate, 6-Hydroxhexanoate or AdipateSemialdehyde as Central Precursor to Hexamethylenediamine

In some embodiments, hexamethylenediamine is synthesized from thecentral precursor, 6-aminohexanoate, by conversion of 6-aminohexanoateto 6-aminohexanal by a carboxylate reductase classified, for example,under EC 1.2.99.6 such as the gene product of car (see above) incombination with a phosphopantetheine transferase enhancer (e.g.,encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO:14) genefrom Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ IDNO:15) gene from Nocardia) or the gene product of GriC & GriD; followedby conversion of 6-s aminohexanal to hexamethylenediamine by aω-transaminase (e.g., classified, for example, under EC 2.6.1.18, EC2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as SEQ IDNOs:8-13, see above). See FIG. 4.

The carboxylate reductase encoded by the gene product of car and thephosphopantetheine transferase enhancer npt or sfp has broad substratespecificity, including terminal difunctional C4 and C5 carboxylic acids(Venkitasubramanian et al., Enzyme and Microbial Technology, 2008, 42,130-137).

In some embodiments, hexamethylenediamine is synthesized from thecentral precursor, 6-hydroxhexanoate (which can be produced as describedin FIG. 5), by conversion of 6-hydroxhexanoate to 6-hydroxhexanal by acarboxylate reductase classified, for example, under EC 1.2.99.6 such asthe gene product of car (see above) in combination with aphosphopantetheine transferase enhancer (e.g., encoded by a sfp genefrom Bacillus subtilis or npt gene from Nocardia) or the gene product ofGriC & GriD (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387);followed by conversion of 6-aminohexanal to 6-aminohexanol by aω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19,EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as SEQ ID NOs:8-13, seeabove; followed by conversion to 6-aminohexanal by an alcoholdehydrogenase classified, for example, under EC 1.1.1.—(e.g., EC1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as the geneproduct of YMR318C (classified, for example, under EC 1.1.1.2, seeGenbank Accession No. CAA90836.1) or YqhD (from E. coli, GenBankAccession No. AAA69178.1) (Liu et al., Microbiology, 2009, 155,2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; Jarboe,2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the proteinhaving GenBank Accession No. CAA81612.1 (from Geobacillusstearothermophilus); followed by conversion to hexamethylenediamine by aω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19,EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as SEQ ID NOs:8-13, seeabove. See FIG. 4.

In some embodiments, hexamethylenediamine is synthesized from thecentral precursor, 6-aminohexanoate, by conversion of 6-aminohexanoateto N6-acetyl-6-aminohexanoate by a N-acetyltransferase such as a lysineN-acetyltransferase classified, for example, under EC 2.3.1.32; followedby conversion to N6-acetyl-6-aminohexanal by a carboxylate reductaseclassified, for example, under EC 1.2.99.6 such as the gene product ofcar (see above) in combination with a phosphopantetheine transferaseenhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt genefrom Nocardia) or the gene product of GriC & GriD; followed byconversion to N6-acetyl-1,6-diaminohexane by a ω-transaminaseclassified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC2.6.1.48, EC 2.6.1.46, or EC 2.6.1.82 such as SEQ ID NOs:8-13, seeabove; followed by conversion to hexamethylenediamine by anacetylputrescine deacylase classified, for example, under EC 3.5.1.62.See, FIG. 4.

In some embodiments, hexamethylenediamine is synthesized from thecentral precursor, adipate semialdehyde, by conversion of adipatesemialdehyde to hexanedial by a carboxylate reductase classified, forexample, under EC 1.2.99.6 such as the gene product of car (see above)in combination with a phosphopantetheine transferase enhancer (e.g.,encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia)or the gene product of GriC & GriD; followed by conversion to6-aminohexanal by a ω-transaminase classified, for example, under EC2.6.1.18, EC 2.6.1.19, or EC 2.6.1.48; followed by conversion tohexamethylenediamine by a ω-transaminase classified, for example, underEC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, EC 2.6.1.46, or EC2.6.1.82 such as SEQ ID NOs:8-13, see above. See FIG. 4.

Pathways Using Adipate or Adipate Semialdehyde as Central Precursor to1,6-Hexanediol

In some embodiments, 6-hydroxhexanoate is synthesized from the centralprecursor, adipate, by conversion of adipate to adipate semialdehyde bya carboxylate reductase classified, for example, under EC 1.2.99.6 suchas the gene product of car (see above) in combination with aphosphopantetheine transferase enhancer (e.g., encoded by a sfp genefrom Bacillus subtilis or npt gene from Nocardia) or the gene product ofGriC & GriD; followed by conversion to 6-hydroxhexanoate by adehydrogenase classified, for example, under EC 1.1.1.—such as a6-hydroxyhexanoate dehydrogenase classified, for example, under EC1.1.1.258 such as the gene from of ChnD or a 5-hydroxypentanoatedehydrogenase classified, for example, under EC 1.1.1.—such as the geneproduct of CpnD (see, for example, Iwaki et al., 2002, Appl. Environ.Microbiol., 68(11):5671-5684) or a 4-hydroxybutyrate dehydrogenase suchas gabD (see, for example, Lütke-Eversloh & Steinbüchel, 1999, FEMSMicrobiology Letters, 181(1):63-71). See FIG. 5. Adipate semialdehydealso can be produced from adipyl-CoA using an acetylating aldehydedehydrogenase as described above. See, also FIG. 5.

In some embodiments, 1,6 hexanediol is synthesized from the centralprecursor, 6-hydroxhexanoate, by conversion of 6-hydroxhexanoate to6-hydroxhexanal by a carboxylate reductase classified, for example,under EC 1.2.99.6 such as the gene product of car (see above) incombination with a phosphopantetheine transferase enhancer (e.g.,encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia)or the gene product of GriC & GriD; followed by conversion of6-hydroxhexanal to 1,6 hexanediol by an alcohol dehydrogenaseclassified, for example, under EC 1.1.1.—such as EC 1.1.1.1, EC 1.1.1.2,EC 1.1.1.21, or EC 1.1.1.184) such as the gene product of YMR318C orYqhD (see, e.g., Liu et al., Microbiology, 2009, 155, 2078-2085; Larroyet al., 2002, Biochem J., 361(Pt 1), 163-172; or Jarboe, 2011, Appl.Microbiol. Biotechnol., 89(2), 249-257) or the protein having GenBankAccession No. CAA81612.1 (from Geobacillus stearothermophilus). See,FIG. 6.

Cultivation Strategy

In some embodiments, the cultivation strategy entails achieving anaerobic, anaerobic or micro-aerobic cultivation condition.

In some embodiments, the cultivation strategy entails nutrientlimitation such as nitrogen, phosphate or oxygen limitation.

In some embodiments, a cell retention strategy using, for example,ceramic hollow fiber membranes can be employed to achieve and maintain ahigh cell density during either fed-batch or continuous fermentation.

In some embodiments, the principal carbon source fed to the fermentationin the synthesis of one or more C6 building blocks can derive frombiological or non-biological feedstocks.

In some embodiments, the biological feedstock can be, can include, orcan derive from, monosaccharides, disaccharides, lignocellulose,hemicellulose, cellulose, lignin, levulinic acid and formic acid,triglycerides, glycerol, fatty acids, agricultural waste, condenseddistillers' solubles, or municipal waste.

The efficient catabolism of crude glycerol stemming from the productionof biodiesel has been demonstrated in several microorganisms such asEscherichia coli, Cupriavidus necator, Pseudomonas oleavorans,Pseudomonas putida and Yarrowia lipolytica (Lee et al., Appl. Biochem.Biotechnol., 2012, 166, 1801-1813; Yang et al., Biotechnology forBiofuels, 2012, 5:13; Meijnen et al., Appl. Microbiol. Biotechnol.,2011, 90, 885-893).

The efficient catabolism of lignocellulosic-derived levulinic acid hasbeen demonstrated in several organisms such as Cupriavidus necator andPseudomonas putida in the synthesis of 3-hydroxyvalerate via theprecursor propanoyl-CoA (Jaremko and Yu, Journal of Biotechnology, 2011,155, 2011, 293-298; Martin and Prather, Journal of Biotechnology, 2009,139, 61-67).

The efficient catabolism of lignin-derived aromatic compounds such asbenzoate analogues has been demonstrated in several microorganisms suchas Pseudomonas putida, Cupriavidus necator (Bugg et al., Current Opinionin Biotechnology, 2011, 22, 394-400; Pérez-Pantoja et al., FEMSMicrobiol. Rev., 2008, 32, 736-794).

The efficient utilization of agricultural waste, such as olive millwaste water has been demonstrated in several microorganisms, includingYarrowia lipolytica (Papanikolaou et al., Bioresour. Technol., 2008,99(7), 2419-2428).

The efficient utilization of fermentable sugars such as monosaccharidesand disaccharides derived from cellulosic, hemicellulosic, cane and beetmolasses, cassava, corn and other agricultural sources has beendemonstrated for several microorganism such as Escherichia coli,Corynebacterium glutamicum and Lactobacillus delbrueckii and Lactococcuslactis (see, e.g., Hermann et al, Journal of Biotechnology, 2003, 104,155-172; Wee et al., Food Technol. Biotechnol., 2006, 44(2), 163-172;Ohashi et al., Journal of Bioscience and Bioengineering, 1999, 87(5),647-654).

The efficient utilization of furfural, derived from a variety ofagricultural lignocellulosic sources, has been demonstrated forCupriavidus necator (Li et al., Biodegradation, 2011, 22, 1215-1225).

In some embodiments, the non-biological feedstock can be or can derivefrom natural gas, syngas, CO₂/H₂, methanol, ethanol, benzoic acid,non-volatile residue (NVR), a caustic wash waste stream from cyclohexaneoxidation processes, or terephthalic acid/isophthalic acid mixture wastestreams.

The efficient catabolism of methanol has been demonstrated for themethylotrophic yeast Pichia pastoris.

The efficient catabolism of ethanol has been demonstrated forClostridium kluyveri (Seedorf et al., Proc. Natl. Acad. Sci. USA, 2008,105(6) 2128-2133).

The efficient catabolism of CO₂ and H₂, which may be derived fromnatural gas and other chemical and petrochemical sources, has beendemonstrated for Cupriavidus necator (Prybylski et al., Energy,Sustainability and Society, 2012, 2:11).

The efficient catabolism of syngas has been demonstrated for numerousmicroorganisms, such as Clostridium ljungdahlii and Clostridiumautoethanogenum (Köpke et al., Applied and Environmental Microbiology,2011, 77(15), 5467-5475).

The efficient catabolism of the non-volatile residue waste stream fromcyclohexane processes has been demonstrated for numerous microorganisms,such as Delftia acidovorans and Cupriavidus necator (Ramsay et al.,Applied and Environmental Microbiology, 1986, 52(1), 152-156).

In some embodiments, the host microorganism is a prokaryote. Forexample, the prokaryote can be a bacterium from the genus Escherichiasuch as Escherichia coli; from the genus Clostridia such as Clostridiumljungdahlii, Clostridium autoethanogenum or Clostridium kluyveri; fromthe genus Corynebacteria such as Corynebacterium glutamicum; from thegenus Cupriavidus such as Cupriavidus necator or Cupriavidusmetallidurans; from the genus Pseudomonas such as Pseudomonasfluorescens, Pseudomonas putida or Pseudomonas oleavorans; from thegenus Delftia such as Delftia acidovorans; from the genus Bacillus suchas Bacillus subtillis; from the genus Lactobacillus such asLactobacillus delbrueckii; or from the genus Lactococcus such asLactococcus lactis. Such prokaryotes also can be a source of genes toconstruct recombinant host cells described herein that are capable ofproducing one or more C6 building blocks.

In some embodiments, the host microorganism is a eukaryote. For example,the eukaryote can be a filamentous fungus, e.g., one from the genusAspergillus such as Aspergillus niger. Alternatively, the eukaryote canbe a yeast, e.g., one from the genus Saccharomyces such as Saccharomycescerevisiae; from the genus Pichia such as Pichia pastoris; or from thegenus Yarrowia such as Yarrowia lipolytica; from the genus Issatchenkiasuch as Issathenkia orientalis; from the genus Debaryomyces such asDebaryomyces hansenii; from the genus Arxula such as Arxulaadenoinivorans; or from the genus Kluyveromyces such as Kluyveromyceslactis. Such eukaryotes also can be a source of genes to constructrecombinant host cells described herein that are capable of producingone or more C6 building blocks.

Metabolic Engineering

The present document provides methods involving less than all the stepsdescribed for all the above pathways. Such methods can involve, forexample, one, two, three, four, five, six, seven, eight, nine, ten,eleven, twelve or more of such steps. Where less than all the steps areincluded in such a method, the first, and in some embodiments the only,step can be any one of the steps listed.

Furthermore, recombinant hosts described herein can include anycombination of the above enzymes such that one or more of the steps,e.g., one, two, three, four, five, six, seven, eight, nine, ten, or moreof such steps, can be performed within a recombinant host. This documentprovides host cells of any of the genera and species listed andgenetically engineered to express one or more (e.g., two, three, four,five, six, seven, eight, nine, 10, 11, 12 or more) recombinant forms ofany of the enzymes recited in the document. Thus, for example, the hostcells can contain exogenous nucleic acids encoding enzymes catalyzingone or more of the steps of any of the pathways described herein.

In addition, this document recognizes that where enzymes have beendescribed as accepting CoA-activated substrates, analogous enzymeactivities associated with [acp]-bound substrates exist that are notnecessarily in the same enzyme class.

Also, this document recognizes that where enzymes have been describedaccepting (R)-enantiomers of substrate, analogous enzyme activitiesassociated with (S)-enantiomer substrates exist that are not necessarilyin the same enzyme class.

This document also recognizes that where an enzyme is shown to accept aparticular co-factor, such as NADPH, or a co-substrate, such asacetyl-CoA, many enzymes are promiscuous in terms of accepting a numberof different co-factors or co-substrates in catalyzing a particularenzyme activity. Also, this document recognizes that where enzymes havehigh specificity for e.g., a particular co-factor such as NADH, anenzyme with similar or identical activity that has high specificity forthe co-factor NADPH may be in a different enzyme class.

In some embodiments, the enzymes in the pathways outlined herein are theresult of enzyme engineering via non-direct or rational enzyme designapproaches with aims of improving activity, improving specificity,reducing feedback inhibition, reducing repression, improving enzymesolubility, changing stereo-specificity, or changing co-factorspecificity.

In some embodiments, the enzymes in the pathways outlined herein can begene dosed (i.e., overexpressed by having a plurality of copies of thegene in the host organism), into the resulting genetically modifiedorganism via episomal or chromosomal integration approaches.

In some embodiments, genome-scale system biology techniques such as FluxBalance Analysis can be utilized to devise genome scale attenuation orknockout strategies for directing carbon flux to a C6 building block.

Attenuation strategies include, but are not limited to; the use oftransposons, homologous recombination (double cross-over approach),mutagenesis, enzyme inhibitors and RNA interference (RNAi).

In some embodiments, fluxomic, metabolomic and transcriptomal data canbe utilized to inform or support genome-scale system biology techniques,thereby devising genome scale attenuation or knockout strategies indirecting carbon flux to a C6 building block.

In some embodiments, the host microorganism's tolerance to highconcentrations of a C6 building block can be improved through continuouscultivation in a selective environment.

In some embodiments, the host microorganism's endogenous biochemicalnetwork can be attenuated or augmented to (1) ensure the intracellularavailability of oxalyl-CoA, acetyl-CoA, and/or malonyl-CoA, (2) createan NADH or NADPH imbalance that may only be balanced via the formationof one or more C6 building blocks, (3) prevent degradation of centralmetabolites, central precursors leading to and including one or more C6building blocks and/or (4) ensure efficient efflux from the cell.

In some embodiments requiring intracellular availability of oxaloyl-CoAfor C6 building block synthesis, an oxaloacetase can be overexpressed inthe host (Han et al., 2007, J. Biol. Chem., 282, 9581-9590).

In some embodiments requiring the intracellular availability ofoxalyl-CoA, a PEP carboxykinase or PEP carboxylase can be overexpressedin the host to generate anaplerotic carbon flux into the Krebs cycletowards oxaloacetate (Schwartz et al., 2009, Proteomics, 9, 5132-5142).

In some embodiments requiring the intracellular availability ofoxalyl-CoA, a pyruvate carboxylase can be overexpressed in the host togenerated anaplerotic carbon flux into the Krebs cycle towardsoxaloacetate (Schwartz et al., 2009, supra).

In some embodiments requiring the intracellular availability ofoxalyl-CoA, a PEP synthase can be overexpressed in the host to enhancethe flux from pyruvate to PEP, thus increasing the carbon flux into theKrebs cycle via PEP carboxykinase or PEP carboxylase (Schwartz et al.,2009, supra).

In some embodiments requiring intracellular availability of acetyl-CoAfor C6 building block synthesis, endogenous enzymes catalyzing thehydrolysis acetyl-CoA such as short-chain length thioesterases can beattenuated in the host organism.

In some embodiments requiring the intracellular availability ofacetyl-CoA for C6 building block synthesis, an endogenousphosphotransacetylase generating acetate such as pta can be attenuated(Shen et al., Appl. Environ. Microbiol., 2011, 77(9):2905-2915).

In some embodiments requiring the intracellular availability ofacetyl-CoA for C6 building block synthesis, an endogenous gene in anacetate synthesis pathway encoding an acetate kinase, such as ack, canbe attenuated.

In some embodiments requiring the intracellular availability ofacetyl-CoA and NADH for C6 building block synthesis, an endogenous geneencoding an enzyme that catalyzes the degradation of pyruvate to lactatesuch as a lactate dehydrogenase encoded by ldhA can be attenuated (Shenet al., 2011, supra).

In some embodiments requiring the intracellular availability ofacetyl-CoA and NADH for C6 building block synthesis, endogenous genesencoding enzymes, such as menaquinol-fumarate oxidoreductase, thatcatalyze the degradation of phophoenolpyruvate to succinate such asfrdBC can be attenuated (see, e.g., Shen et al., 2011, supra).

In some embodiments requiring the intracellular availability ofacetyl-CoA and NADH for C6 building block synthesis, an endogenous geneencoding an enzyme that catalyzes the degradation of acetyl-CoA toethanol such as the alcohol dehydrogenase encoded by adhE can beattenuated (Shen et al., 2011, supra).

In some embodiments, where pathways require excess NADH co-factor for C6building block synthesis, a recombinant formate dehydrogenase gene canbe overexpressed in the host organism (Shen et al., 2011, supra).

In some embodiments, where pathways require excess NADH or NADPHco-factor for C6 building block synthesis, an endogenoustranshydrogenase dissipating the co-factor imbalance can be attenuated.

In some embodiments, an endogenous gene encoding an enzyme thatcatalyzes the degradation of pyruvate to ethanol such as pyruvatedecarboxylase can be attenuated.

In some embodiments, an endogenous gene encoding an enzyme thatcatalyzes the generation of isobutanol such as a 2-oxoacid decarboxylasecan be attenuated.

In some embodiments requiring the intracellular availability ofacetyl-CoA for C6 building block synthesis, a recombinant acetyl-CoAsynthetase such as the gene product of acs can be overexpressed in themicroorganism (Satoh et al., J. Bioscience and Bioengineering, 2003,95(4):335-341).

In some embodiments, carbon flux can be directed into the pentosephosphate cycle to increase the supply of NADPH by attenuating anendogenous glucose-6-phosphate isomerase (EC 5.3.1.9).

In some embodiments, carbon flux can be redirected into the pentosephosphate cycle to increase the supply of NADPH by overexpression a6-phosphogluconate dehydrogenase and/or a transketolase (Lee et al.,2003, Biotechnology Progress, 19(5), 1444-1449).

In some embodiments, where pathways require excess NADPH co-factor inthe synthesis of a C6 building block, a gene such as UdhA encoding apuridine nucleotide transhydrogenase can be overexpressed in the hostorganisms (Brigham et al., Advanced Biofuels and Bioproducts, 2012,Chapter 39, 1065-1090).

In some embodiments, where pathways require excess NADPH co-factor inthe synthesis of a C6 Building Block, a recombinantglyceraldehyde-3-phosphate-dehydrogenase gene such as GapN can beoverexpressed in the host organisms (Brigham et al., 2012, supra).

In some embodiments, where pathways require excess NADPH co-factor inthe synthesis of a C6 building block, a recombinant malic enzyme genesuch as maeA or maeB can be overexpressed in the host organisms (Brighamet al., 2012, supra).

In some embodiments, where pathways require excess NADPH co-factor inthe synthesis of a C6 building block, a recombinant glucose-6-phosphatedehydrogenase gene such as zwf can be overexpressed in the hostorganisms (Lim et al., J. Bioscience and Bioengineering, 2002, 93(6),543-549).

In some embodiments, where pathways require excess NADPH co-factor inthe synthesis of a C6 building block, a recombinant fructose 1,6diphosphatase gene such as fbp can be overexpressed in the hostorganisms (Becker et al., J. Biotechnol., 2007, 132:99-109).

In some embodiments, where pathways require excess NADPH co-factor inthe synthesis of a C6 building block, endogenous triose phosphateisomerase (EC 5.3.1.1) can be attenuated.

In some embodiments, where pathways require excess NADPH co-factor inthe synthesis of a C6 building block, a recombinant glucosedehydrogenase such as the gene product of gdh can be overexpressed inthe host organism (Satoh et al., J. Bioscience and Bioengineering, 2003,95(4):335-341).

In some embodiments, endogenous enzymes facilitating the conversion ofNADPH to NADH can be attenuated, such as the NADH generation cycle thatmay be generated via inter-conversion of glutamate dehydrogenasesclassified under EC 1.4.1.2 (NADH-specific) and EC 1.4.1.4(NADPH-specific). For example, avoiding dissipation of an NADH imbalancetowards C6 building blocks, a NADPH-specific glutamate dehydrogenase canbe attenuated.

In some embodiments, an endogenous glutamate dehydrogenase (EC 1.4.1.3)that utilizes both NADH and NADPH as co-factors can be attenuated.

In some embodiments, a membrane-bound enoyl-CoA reductases can besolubilized via expression as a fusion protein to a small solubleprotein such as a maltose binding protein (Gloerich et al., FEBSLetters, 2006, 580, 2092-2096).

In some embodiments using hosts that naturally accumulatepolyhydroxyalkanoates, the endogenous polymer synthase enzymes can beattenuated in the host strain.

In some embodiments, a L-alanine dehydrogenase can be overexpressed inthe host to regenerate L-alanine from pyruvate as an amino donor forω-transaminase reactions.

In some embodiments, a L-glutamate dehydrogenase specific for theco-factor used to achieve co-factor imbalance can be overexpressed inthe host to regenerate L-glutamate from 2-oxoglutarate as an amino donorfor ω-transaminase reactions. For example, promoting dissipation of theNADH imbalance towards C6 building blocks, a NADH-specific glutamatedehydrogenase can be overexpressed.

In some embodiments, enzymes such as pimeloyl-CoA dehydrogenaseclassified under, EC 1.3.1.62; an acyl-CoA dehydrogenase classified, forexample, under EC 1.3.8.7 or EC 1.3.8.1; and/or a glutaryl-CoAdehydrogenase classified, for example, under EC 1.3.8.6 that degradecentral metabolites and central precursors leading to and including C6building blocks can be attenuated.

In some embodiments, endogenous enzymes activating C6 building blocksvia Coenzyme A esterification such as CoA-ligases (e.g., a pimeloyl-CoAsynthetase) classified under, for example, EC 6.2.1.14 can beattenuated.

In some embodiments, a methanol dehydrogenase and a formaldehydedehydrogenase can be overexpressed in the host to allow methanolcatabolism via formate.

In some embodiments, an S-adenosylmethionine synthetase can beoverexpressed in the host to generate S-Adenosyl-L-methionine asaco-factor for malonyl-[acp] O-methyltransferase.

In some embodiments, the efflux of a C6 building block across the cellmembrane to the extracellular media can be enhanced or amplified bygenetically engineering structural modifications to the cell membrane orincreasing any associated transporter activity for a C6 building block.

The efflux of hexamethylenediamine can be enhanced or amplified byoverexpressing broad substrate range multidrug transporters such as Bltfrom Bacillus subtilis (Woolridge et al., 1997, J. Biol. Chem.,272(14):8864-8866); AcrB and AcrD from Escherichia coli (Elkins &Nikaido, 2002, J. Bacteriol., 184(23), 6490-6499), NorA fromStaphylococcus aereus (Ng et al., 1994, Antimicrob Agents Chemother,38(6), 1345-1355), or Bmr from Bacillus subtilis (Neyfakh, 1992,Antimicrob Agents Chemother, 36(2), 484-485).

The efflux of 6-aminohexanoate and hexamethylenediamine can be enhancedor amplified by overexpressing the solute transporters such as the lysEtransporter from Corynebacterium glutamicum (Bellmann et al., 2001,Microbiology, 147, 1765-1774).

The efflux of adipic acid can be enhanced or amplified by overexpressinga dicarboxylate transporter such as the SucE transporter fromCorynebacterium glutamicum (Huhn et al., Appl. Microbiol. & Biotech.,89(2), 327-335).

Producing C6 Building Blocks Using a Recombinant Host

Typically, one or more C6 building blocks can be produced by providing ahost microorganism and culturing the provided microorganism with aculture medium containing a suitable carbon source as described above.In general, the culture media and/or culture conditions can be such thatthe microorganisms grow to an adequate density and produce a C6 buildingblock efficiently. For large-scale production processes, any method canbe used such as those described elsewhere (Manual of IndustrialMicrobiology and Biotechnology, 2^(nd) Edition, Editors: A. L. Demainand J. E. Davies, ASM Press; and Principles of Fermentation Technology,P. F. Stanbury and A. Whitaker, Pergamon). Briefly, a large tank (e.g.,a 100 gallon, 200 gallon, 500 gallon, or more tank) containing anappropriate culture medium is inoculated with a particularmicroorganism. After inoculation, the microorganism is incubated toallow biomass to be produced. Once a desired biomass is reached, thebroth containing the microorganisms can be transferred to a second tank.This second tank can be any size. For example, the second tank can belarger, smaller, or the same size as the first tank. Typically, thesecond tank is larger than the first such that additional culture mediumcan be added to the broth from the first tank. In addition, the culturemedium within this second tank can be the same as, or different from,that used in the first tank.

Once transferred, the microorganisms can be incubated to allow for theproduction of a C6 building block. Once produced, any method can be usedto isolate C6 building blocks. For example, C6 building blocks can berecovered selectively from the fermentation broth via adsorptionprocesses. In the case of adipic acid and 6-aminohexanoic acid, theresulting eluate can be further concentrated via evaporation,crystallized via evaporative and/or cooling crystallization, and thecrystals recovered via centrifugation. In the case ofhexamethylenediamine and 1,6-hexanediol, distillation may be employed toachieve the desired product purity.

The invention is further described in the following example, which doesnot limit the scope of the invention described in the claims.

EXAMPLES Example 1 Enzyme Activity of Thioesterases Using Adipyl-CoA asa Substrate and Forming Adipate

A sequence encoding an N-terminal His-tag was added to the genes fromEscherichia coli encoding the thioesterases of SEQ ID NOs: 1 and 2respectively (see FIG. 7A), such that an N-terminal HIS taggedthioesterase could be produced. Each of the resulting modified genes wascloned into a pET15b expression vector under control of the T7 promoter.Each expression vector was transformed into a BL21[DE3] E. coli host.The resulting recombinant E. coli strains were cultivated at 37° C. in a500 mL shake flask culture containing 50 mL Luria Broth (LB) media andantibiotic selection pressure, with shaking at 230 rpm. The culture wasinduced overnight at 17° C. using 0.5 mM IPTG.

The pellet from the induced shake flask culture was harvested viacentrifugation. The pellet was resuspended and lysed in Y-per™ solution(ThermoScientific, Rockford, Ill.). The cell debris was separated fromthe supernatant via centrifugation. The thioesterases were purified fromthe supernatant using Ni-affinity chromatography and the eluate wasbuffer exchanged and concentrated via ultrafiltration.

The enzyme activity assay was performed in triplicate in a buffercomposed of 50 mM phosphate buffer (pH=7.4), 0.1 mM Ellman's reagent,and 667 μM of adipyl-CoA (as substrate). Each enzyme activity assayreaction was initiated by adding 0.8 μM of the gene product of SEQ ID NO1 and 4.1 μM of the gene product of SEQ ID NO 2 to the assay buffercontaining the adipyl-CoA and incubating at 37° C. for 20 min. Therelease of Coenzyme A was monitored by absorbance at 412 nm. Theabsorbance associated with the substrate only control, which containedboiled enzyme, was subtracted from the active enzyme assay absorbanceand compared to the empty vector control. The gene product of SEQ ID NO1 and SEQ ID NO 2 accepted adipyl-CoA as substrate as confirmed viarelative spectrophotometry (see FIG. 8) and synthesized adipate as areaction product.

Example 2 Enzyme Activity of ω-Transaminase Using Adipate Semialdehydeas Substrate and Forming 6-Aminohexanoate

A nucleotide sequence encoding a His-tag was added to the genes fromChromobacterium violaceum, Pseudomonas aeruginosa, Pseudomonas syringae,Rhodobacter sphaeroides, and Vibrio fluvialis encoding theω-transaminases of SEQ ID NOs: 7, 8, 9, 10 and 12, respectively (seeFIGS. 7E and 7F) such that N-terminal HIS tagged ω-transaminases couldbe produced. Each of the resulting modified genes was cloned into apET21a expression vector under control of the T7 promoter and eachexpression vector was transformed into a BL21[DE3] E. coli host. Theresulting recombinant E. coli strains were cultivated at 37° C. in a 250mL shake flask culture containing 50 mL LB media and antibioticselection pressure, with shaking at 230 rpm. Each culture was inducedovernight at 16° C. using 1 mM IPTG.

The pellet from each induced shake flask culture was harvested viacentrifugation. Each pellet was resuspended and lysed via sonication.The cell debris was separated from the supernatant via centrifugationand the cell free extract was used immediately in enzyme activityassays.

Enzyme activity assays in the reverse direction (i.e., 6-aminohexanoateto adipate semialdehyde) were performed in a buffer composed of a finalconcentration of 50 mM HEPES buffer (pH=7.5), 10 mM 6-aminohexanoate, 10mM pyruvate and 100 μM pyridoxyl 5′ phosphate. Each enzyme activityassay reaction was initiated by adding cell free extract of theω-transaminase gene product or the empty vector control to the assaybuffer containing the 6-aminohexanoate and incubated at 25° C. for 24 h,with shaking at 250 rpm. The formation of L-alanine from pyruvate wasquantified via RP-HPLC.

Each enzyme only control without 6-aminohexanoate demonstrated low baseline conversion of pyruvate to L-alanine. See FIG. 14. The gene productof SEQ ID NO 7, SEQ ID NO 9, SEQ ID NO 10 and SEQ ID NO 12 accepted6-aminohexanote as substrate as confirmed against the empty vectorcontrol. See FIG. 15.

Enzyme activity in the forward direction (i.e., adipate semialdehyde to6-aminohexanoate) was confirmed for the transaminases of SEQ ID NO 7,SEQ ID NO 8, SEQ ID NO 9, SEQ ID NO 10 and SEQ ID NO 12. Enzyme activityassays were performed in a buffer composed of a final concentration of50 mM HEPES buffer (pH=7.5), 10 mM adipate semialdehyde, 10 mM L-alanineand 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reactionwas initiated by adding a cell free extract of the ω-transaminase geneproduct or the empty vector control to the assay buffer containing theadipate semialdehyde and incubated at 25° C. for 4 h, with shaking at250 rpm. The formation of pyruvate was quantified via RP-HPLC.

The gene product of SEQ ID NO 7, SEQ ID NO 8, SEQ ID NO 9, SEQ ID NO 10and SEQ ID NO 12 accepted adipate semialdehyde as substrate as confirmedagainst the empty vector control. See FIG. 16. The reversibility of theω-transaminase activity was confirmed, demonstrating that theω-transaminases of SEQ ID NO 7, SEQ ID NO 8, SEQ ID NO 9, SEQ ID NO 10and SEQ ID NO 12 accepted adipate semialdehyde as substrate andsynthesized 6-aminohexanoate as a reaction product.

Example 3 Enzyme Activity of Carboxylate Reductase Using Adipate asSubstrate and Forming Adipate Semialdehyde

A nucleotide sequence encoding a HIS-tag was added to the genes fromSegniliparus rugosus and Segniliparus rotundus that encode thecarboxylate reductases of SEQ ID NOs: 5 and 7, respectively (see FIGS.7C and 7E), such that N-terminal HIS tagged carboxylate reductases couldbe produced. Each of the modified genes was cloned into a pET Duetexpression vector along with a sfp gene encoding a HIS-taggedphosphopantetheine transferase from Bacillus subtilis, both under the T7promoter. Each expression vector was transformed into a BL21[DE3] E.coli host and the resulting recombinant E. coli strains were cultivatedat 37° C. in a 250 mL shake flask culture containing 50 mL LB media andantibiotic selection pressure, with shaking at 230 rpm. Each culture wasinduced overnight at 37° C. using an auto-induction media.

The pellet from each induced shake flask culture was harvested viacentrifugation. Each pellet was resuspended and lysed via sonication,and the cell debris was separated from the supernatant viacentrifugation. The carboxylate reductases and phosphopantetheinetransferases were purified from the supernatant using Ni-affinitychromatography, diluted 10-fold into 50 mM HEPES buffer (pH=7.5), andconcentrated via ultrafiltration.

Enzyme activity assays (i.e., from adipate to adipate semialdehyde) wereperformed in triplicate in a buffer composed of a final concentration of50 mM HEPES buffer (pH=7.5), 2 mM adipate, 10 mM MgCl₂, 1 mM ATP and 1mM NADPH. Each enzyme activity assay reaction was initiated by addingpurified carboxylate reductase and phosphopantetheine transferase geneproducts or the empty vector control to the assay buffer containing theadipate and then incubated at room temperature for 20 min. Theconsumption of NADPH was monitored by absorbance at 340 nm. Each enzymeonly control without adipate demonstrated low base line consumption ofNADPH. See FIG. 9.

The gene products of SEQ ID NO 5 and SEQ ID NO 7, enhanced by the geneproduct of sfp, accepted adipate as substrate, as confirmed against theempty vector control (see FIG. 10), and synthesized adipatesemialdehyde.

Example 4 Enzyme Activity of Carboxylate Reductase Using6-Hydroxyhexanoate as Substrate and Forming 6-Hydroxyhexanal

A nucleotide sequence encoding a His-tag was added to the genes fromMycobacterium marinum, Mycobacterium smegmatis, Mycobacterium smegmatis,Segniliparus rugosus, Mycobacterium massiliense, and Segniliparusrotundus that encode the carboxylate reductases of SEQ ID NOs: 3-7,respectively (see FIGS. 7A-7E) such that N-terminal HIS taggedcarboxylate reductases could be produced. Each of the modified genes wascloned into a pET Duet expression vector alongside a sfp gene encoding aHis-tagged phosphopantetheine transferase from Bacillus subtilis, bothunder control of the T7 promoter. Each expression vector was transformedinto a BL21[DE3] E. coli host. Each resulting recombinant E. coli strainwas cultivated at 37° C. in a 250 mL shake flask culture containing 50mL LB media and antibiotic selection pressure, with shaking at 230 rpm.Each culture was induced overnight at 37° C. using an auto-inductionmedia.

The pellet from each induced shake flask culture was harvested viacentrifugation. Each pellet was resuspended and lysed via sonication.The cell debris was separated from the supernatant via centrifugation.The carboxylate reductases and phosphopantetheine transferase werepurified from the supernatant using Ni-affinity chromatography, diluted10-fold into 50 mM HEPES buffer (pH=7.5) and concentrated viaultrafiltration.

Enzyme activity (i.e., 6-hydroxyhexanoate to 6-hydroxyhexanal) assayswere performed in triplicate in a buffer composed of a finalconcentration of 50 mM HEPES buffer (pH=7.5), 2 mM 6-hydroxyhexanal, 10mM MgCl₂, 1 mM ATP, and 1 mM NADPH. Each enzyme activity assay reactionwas initiated by adding purified carboxylate reductase andphosphopantetheine transferase or the empty vector control to the assaybuffer containing the 6-hydroxyhexanoate and then incubated at roomtemperature for 20 min. The consumption of NADPH was monitored byabsorbance at 340 nm. Each enzyme only control without6-hydroxyhexanoate demonstrated low base line consumption of NADPH. SeeFIG. 9.

The gene products of SEQ ID NO 3-7, enhanced by the gene product of sfp,accepted 6-hydroxyhexanoate as substrate as confirmed against the emptyvector control (see FIG. 11), and synthesized 6-hydroxyhexanal.

Example 5 Enzyme Activity of ω-Transaminase for 6-Aminohexanol, Forming6-Oxohexanol

A nucleotide sequence encoding an N-terminal His-tag was added to theChromobacterium violaceum, Pseudomonas aeruginosa, Pseudomonas syringae,Rhodobacter sphaeroides, Escherichia coli, and Vibrio fluvialis genesencoding the ω-transaminases of SEQ ID NOs: 8-13, respectively (seeFIGS. 7E and 7F) such that N-terminal HIS tagged ω-transaminases couldbe produced. The modified genes were cloned into a pET21a expressionvector under the T7 promoter. Each expression vector was transformedinto a BL21[DE3] E. coli host. Each resulting recombinant E. coli strainwere cultivated at 37° C. in a 250 mL shake flask culture containing 50mL LB media and antibiotic selection pressure, with shaking at 230 rpm.Each culture was induced overnight at 16° C. using 1 mM IPTG.

The pellet from each induced shake flask culture was harvested viacentrifugation. Each pellet was resuspended and lysed via sonication.The cell debris was separated from the supernatant via centrifugationand the cell free extract was used immediately in enzyme activityassays.

Enzyme activity assays in the reverse direction (i.e., 6-aminohexanol to6-oxohexanol) were performed in a buffer composed of a finalconcentration of 50 mM HEPES buffer (pH=7.5), 10 mM 6-aminohexanol, 10mM pyruvate, and 100 μM pyridoxyl 5′ phosphate. Each enzyme activityassay reaction was initiated by adding cell free extract of theω-transaminase gene product or the empty vector control to the assaybuffer containing the 6-aminohexanol and then incubated at 25° C. for 4h, with shaking at 250 rpm. The formation of L-alanine was quantifiedvia RP-HPLC.

Each enzyme only control without 6-aminohexanol had low base lineconversion of pyruvate to L-alanine See FIG. 14.

The gene products of SEQ ID NO 8-13 accepted 6-aminohexanol as substrateas confirmed against the empty vector control (see FIG. 19) andsynthesized 6-oxohexanol as reaction product. Given the reversibility ofthe ω-transaminase activity (see Example 2), it can be concluded thatthe gene products of SEQ ID 8-13 accept 6-aminohexanol as substrate andform 6-oxohexanol.

Example 6 Enzyme Activity of ω-Transaminase Using Hexamethylenediamineas Substrate and Forming 6-Aminohexanal

A nucleotide sequence encoding an N-terminal His-tag was added to theChromobacterium violaceum, Pseudomonas aeruginosa, Pseudomonas syringae,Rhodobacter sphaeroides, Escherichia coli, and Vibrio fluvialis genesencoding the ω-transaminases of SEQ ID NOs: 8-13, respectively (seeFIGS. 7E and 7F) such that N-terminal HIS tagged ω-transaminases couldbe produced. The modified genes were cloned into a pET21a expressionvector under the T7 promoter. Each expression vector was transformedinto a BL21[DE3] E. coli host. Each resulting recombinant E. coli strainwere cultivated at 37° C. in a 250 mL shake flask culture containing 50mL LB media and antibiotic selection pressure, with shaking at 230 rpm.Each culture was induced overnight at 16° C. using 1 mM IPTG.

The pellet from each induced shake flask culture was harvested viacentrifugation. Each pellet was resuspended and lysed via sonication.The cell debris was separated from the supernatant via centrifugationand the cell free extract was used immediately in enzyme activityassays.

Enzyme activity assays in the reverse direction (i.e.,hexamethylenediamine to 6-aminohexanal) were performed in a buffercomposed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mMhexamethylenediamine, 10 mM pyruvate, and 100 μM pyridoxyl 5′ phosphate.Each enzyme activity assay reaction was initiated by adding cell freeextract of the ω-transaminase gene product or the empty vector controlto the assay buffer containing the hexamethylenediamine and thenincubated at 25° C. for 4 h, with shaking at 250 rpm. The formation ofL-alanine was quantified via RP-HPLC.

Each enzyme only control without hexamethylenediamine had low base lineconversion of pyruvate to L-alanine See FIG. 14.

The gene products of SEQ ID NO 8-13 accepted hexamethylenediamine assubstrate as confirmed against the empty vector control (see FIG. 17)and synthesized 6-aminohexanal as reaction product. Given thereversibility of the ω-transaminase activity (see Example 2), it can beconcluded that the gene products of SEQ ID NOs: 8-13 accept6-aminohexanal as substrate and form hexamethylenediamine.

Example 7 Enzyme Activity of Carboxylate Reductase forN6-Acetyl-6-Aminohexanoate, Forming N6-Acetyl-6-Aminohexanal

The activity of each of the N-terminal His-tagged carboxylate reductasesof SEQ ID NOs: 5-7 (see Example 4, and FIGS. 7C-7E) for convertingN6-acetyl-6-aminohexanoate to N6-acetyl-6-aminohexanal was assayed intriplicate in a buffer composed of a final concentration of 50 mM HEPESbuffer (pH=7.5), 2 mM N6-acetyl-6-aminohexanoate, 10 mM MgCl₂, 1 mM ATP,and 1 mM NADPH. The assays were initiated by adding purified carboxylatereductase and phosphopantetheine transferase or the empty vector controlto the assay buffer containing the N6-acetyl-6-aminohexanoate thenincubated at room temperature for 20 min. The consumption of NADPH wasmonitored by absorbance at 340 nm. Each enzyme only control withoutN6-acetyl-6-aminohexanoate demonstrated low base line consumption ofNADPH. See FIG. 9.

The gene products of SEQ ID NO 5-7, enhanced by the gene product of sfp,accepted N6-acetyl-6-aminohexanoate as substrate as confirmed againstthe empty vector control (see FIG. 12), and synthesizedN6-acetyl-6-aminohexanal.

Example 8 Enzyme Activity of ω-Transaminase UsingN6-Acetyl-1,6-Diaminohexane, and Forming N6-Acetyl-6-Aminohexanal

The activity of the N-terminal His-tagged ω-transaminases of SEQ ID NOs:8-13 (see Example 6, and FIGS. 7E and 7F) for convertingN6-acetyl-1,6-diaminohexane to N6-acetyl-6-aminohexanal was assayedusing a buffer composed of a final concentration of 50 mM HEPES buffer(pH=7.5), 10 mM N6-acetyl-1,6-diaminohexane, 10 mM pyruvate and 100 μMpyridoxyl 5′ phosphate. Each enzyme activity assay reaction wasinitiated by adding a cell free extract of the ω-transaminase or theempty vector control to the assay buffer containing theN6-acetyl-1,6-diaminohexane then incubated at 25° C. for 4 h, withshaking at 250 rpm. The formation of L-alanine was quantified viaRP-HPLC.

Each enzyme only control without N6-acetyl-1,6-diaminohexanedemonstrated low base line conversion of pyruvate to L-alanine See FIG.14.

The gene product of SEQ ID NO 8-13 accepted N6-acetyl-1,6-diaminohexaneas substrate as confirmed against the empty vector control (see FIG. 18)and synthesized N6-acetyl-6-aminohexanal as reaction product.

Given the reversibility of the ω-transaminase activity (see example 2),the gene products of SEQ ID 8-13 accept N6-acetyl-6-aminohexanal assubstrate forming N6-acetyl-1,6-diaminohexane.

Example 9 Enzyme Activity of Carboxylate Reductase Using AdipateSemialdehyde as Substrate and Forming Hexanedial

The N-terminal His-tagged carboxylate reductase of SEQ ID NO 7 (seeExample 4 and FIG. 7E) was assayed using adipate semialdehyde assubstrate. The enzyme activity assay was performed in triplicate in abuffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5),2 mM adipate semialdehyde, 10 mM MgCl₂, 1 mM ATP and 1 mM NADPH. Theenzyme activity assay reaction was initiated by adding purifiedcarboxylate reductase and phosphopantetheine transferase or the emptyvector control to the assay buffer containing the adipate semialdehydeand then incubated at room temperature for 20 min. The consumption ofNADPH was monitored by absorbance at 340 nm. The enzyme only controlwithout adipate semialdehyde demonstrated low base line consumption ofNADPH. See FIG. 9.

The gene product of SEQ ID NO 7, enhanced by the gene product of sfp,accepted adipate semialdehyde as substrate as confirmed against theempty vector control (see FIG. 13) and synthesized hexanedial.

Example 10 Enzyme Activity of Pimeloyl-[Acp] Methyl Ester MethylesteraseUsing Adipyl-CoA Methyl Ester as Substrate and Forming Adipyl-CoA

A sequence encoding an C-terminal His-tag was added to the gene fromEscherichia coli encoding the pimeloyl-[acp] methyl ester methylesteraseof SEQ ID NO: 17 (see FIG. 7G) such that C-terminal HIS taggedpimeloyl-[acp] methyl ester methylesterase could be produced. Theresulting modified gene was cloned into a pET28b+ expression vectorunder control of the T7 promoter and the expression vector wastransformed into a BL21[DE3] E. coli host. The resulting recombinant E.coli strain was cultivated at 37° C. in a 500 mL shake flask culturecontaining 100 mL LB media and antibiotic selection pressure, withshaking at 230 rpm. Each culture was induced overnight at 18° C. using0.3 mM IPTG.

The pellet from each induced shake flask culture was harvested viacentrifugation. Each pellet was resuspended and lysed via sonication.The cell debris was separated from the supernatant via centrifugation.The pimeloyl-[acp] methyl ester methylesterase was purified from thesupernatant using Ni-affinity chromatography, buffer exchanged andconcentrated into 20 mM HEPES buffer (pH=7.5) via ultrafiltration andstored at 4° C.

Enzyme activity assays converting adipyl-CoA methyl ester to adipyl-CoAwere performed in triplicate in a buffer composed of a finalconcentration of 25 mM Tris.HCl buffer (pH=7.0) and 5 [mM] adipyl-CoAmethyl ester. The enzyme activity assay reaction was initiated by addingpimeloyl-[acp] methyl ester methylesterase to a final concentration of10 [μM] to the assay buffer containing the adipyl-CoA methyl ester andincubated at 30° C. for 1 h, with shaking at 250 rpm. The formation ofadipyl-CoA was quantified via LC-MS.

The substrate only control without enzyme showed trace quantities of thesubstrate adipyl-CoA. See FIG. 20. The pimeloyl-[acp] methyl estermethylesterase of SEQ ID NO. 17 accepted adipyl-CoA methyl ester assubstrate and synthesized adipyl-CoA as reaction product as confirmedvia LC-MS. See FIG. 20.

Other Embodiments

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

What is claimed is:
 1. A method for biosynthesizing a product selectedfrom the group consisting of adipic acid, 6-aminohexanoate,6-hydroxhexanoate, hexamethylenediamine, caprolactam and 1,6-hexanediol,said method comprising, in a recombinant host, enzymaticallysynthesizing a six carbon chain aliphatic backbone from oxalyl-CoA andeither (i) acetyl-CoA or malonyl-CoA via two cycles of methyl estershielded carbon chain elongation or (ii) malonyl-[acp] via two cycles ofmethyl-ester shielded carbon chain elongation, and enzymatically formingtwo terminal functional groups selected from the group consisting ofcarboxyl, amine, and hydroxyl groups in said backbone, thereby formingthe product, wherein: a polypeptide having the activity of amalonyl-[acp] O-methyltransferase converts oxalyl-CoA to oxalyl-CoAmethyl ester, and each of said two cycles of carbon chain elongationcomprises using a polypeptide having the activity of (i) aβ-ketoacyl-[acp] synthase or a β-ketothiolase, (ii) a 3-oxoacyl-[acp]reductase, an acetoacetyl-CoA reductase, a 3-hydroxyacyl-CoAdehydrogenase or a 3-hydroxybutyryl-CoA dehydrogenase, (iii) anenoyl-CoA hydratase or a 3-hydroxyacyl-[acp] dehydratase, and (iv) anenoyl-[acp] reductase or a trans-2-enoyl-CoA reductase to produceadipyl-CoA methyl ester or adipyl-[acp] methyl ester.
 2. The method ofclaim 1, wherein the six carbon chain aliphatic backbone is adipyl-[acp]or adipyl-CoA.
 3. The method of claim 1, wherein a polypeptide havingthe activity of a pimeloyl-[acp] methyl ester methylesterase removes themethyl group from adipyl-CoA methyl ester or adipyl-[acp] methyl ester.4. The method of claim 1, wherein the polypeptide having the activity ofa malonyl-[acp] O-methyltransferase has at least 70% sequence identityto the amino acid sequence set forth in SEQ ID NO:
 16. 5. The method ofclaim 3, wherein the polypeptide having the activity of a pimeloyl-[acp]methyl ester methylesterase has at least 70% sequence identity to theamino acid sequence set forth in SEQ ID NO:
 17. 6. The method of claim1, wherein said two terminal functional groups are the same.
 7. Themethod of claim 6, wherein said two terminal functional groups are amineor said two terminal functional groups are hydroxyl groups.
 8. Themethod of claim 1, wherein a polypeptide having the activity of a6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, a4-hydroxybutyrate dehydratase, or an alcohol dehydrogenase enzymaticallyforms a hydroxyl group; a polypeptide having the activity of athioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoatedehydrogenase, a 6-oxohexanoate dehydrogenase, a glutaconateCoA-transferase, or a reversible succinyl-CoA ligase enzymatically formsa terminal carboxyl group; or a polypeptide having the activity of aω-transaminase or a deacetylase enzymatically forms an amine group. 9.The method of claim 8, wherein said polypeptide having the activity of athioesterase has at least 70% sequence identity to the amino acidsequence set forth in SEQ ID NO: 1; or said polypeptide having theactivity of ω-transaminase has at least 70% sequence identity to any oneof the amino acid sequences set forth in SEQ ID NOs: 8-13.
 10. Themethod of claim 1, wherein a polypeptide having the activity of acarboxylate reductase, enhanced by a polypeptide having the activity ofa phosphopantetheinyl transferase, forms a terminal aldehyde group as anintermediate in forming the product.
 11. The method of claim 10, whereinsaid polypeptide having the activity of a carboxylate reductase has atleast 70% sequence identity to any one of the amino acid sequences setforth in SEQ ID NOs. 3-7.
 12. The method of claim 1, wherein said methodis performed in a recombinant host by fermentation.
 13. The method ofclaim 12, wherein the principal carbon source fed to the fermentationderives from biological or non-biological feedstocks.
 14. The method ofclaim 13, wherein the biological feedstock is, or derives from,monosaccharides, disaccharides, lignocellulose, hemicellulose,cellulose, lignin, levulinic acid, formic acid, triglycerides, glycerol,fatty acids, agricultural waste, condensed distillers' solubles, ormunicipal waste; or wherein the non-biological feedstock is, or derivesfrom, natural gas, syngas, CO₂/H₂, methanol, ethanol, benzoate,non-volatile residue (NVR) caustic wash waste stream from cyclohexaneoxidation processes, or terephthalic acid/isophthalic acid mixture wastestreams.
 15. The method of claim 12, wherein the host is a prokaryote.16. The method of claim 15, wherein said prokaryote is from the genusEscherichia such as Escherichia coli, from the genus Clostridia such asClostridium ljungdahlii, Clostridium autoethanogenum or Clostridiumkluyveri; from the genus Corynebacteria such as Corynebacteriumglutamicum; from the genus Cupriavidus such as Cupriavidus necator orCupriavidus metallidurans; from the genus Pseudomonas such asPseudomonas fluorescens, Pseudomonas putida or Pseudomonas oleavorans;from the genus Delftia acidovorans, from the genus Bacillus such asBacillus subtillis; from the genes Lactobacillus such as Lactobacillusdelbrueckii; from the genus Lactococcus such as Lactococcus lactis orfrom the genus Rhodococcus such as Rhodococcus equi.
 17. The method ofclaim 12, wherein the host is a eukaryote.
 18. The method of claim 17,wherein said eukaryote is from the genus Aspergillus such as Aspergillusniger, from the genus Saccharomyces such as Saccharomyces cerevisiae;from the genus Pichia such as Pichia pastoris; from the genus Yarrowiasuch as Yarrowia lipolytica, from the genus Issatchenkia such asIssathenkia orientalis, from the genus Debaryomyces such as Debaryomyceshansenii, from the genus Arxula such as Arxula adenoinivorans, or fromthe genus Kluyveromyces such as Kluyveromyces lactis.
 19. The method ofclaim 12, wherein said host comprises one or more polypeptides havingthe activity of the following attenuated enzymes: polyhydroxyalkanoatesynthase, an acetyl-CoA thioesterase, a phosphotransacetylase formingacetate, an acetate kinase, a lactate dehydrogenase, amenaquinol-fumarate oxidoreductase, a 2-oxoacid decarboxylase producingisobutanol, an alcohol dehydrogenase forming ethanol, a triose phosphateisomerase, a pyruvate decarboxylase, a glucose-6-phosphate isomerase, atranshydrogenase dissipating the NADH or NADPH imbalance, an glutamatedehydrogenase dissipating the NADH or NADPH imbalance, aNADH/NADPH-utilizing glutamate dehydrogenase, a pimeloyl-CoAdehydrogenase; an acyl-CoA dehydrogenase accepting C6 building blocksand central precursors as substrates; a glutaryl-CoA dehydrogenase; or apimeloyl-CoA synthetase; and/or wherein said host overexpresses one ormore genes encoding a polypeptide having the activity of: anoxaloacetase, a PEP carboxylase, a PEP carboxykinase, a pyruvatecarboxylase, a PEP synthase, an acetyl-CoA synthetase, a6-phosphogluconate dehydrogenase; a transketolase; a puridine nucleotidetranshydrogenase; a formate dehydrogenase; aglyceraldehyde-3P-dehydrogenase; a malic enzyme; a glucose-6-phosphatedehydrogenase; a fructose 1,6 diphosphatase; a L-alanine dehydrogenase;a L-glutamate dehydrogenase specific to the NADH or NADPH used togenerate a co-factor imbalance; a methanol dehydrogenase; a formaldehydedehydrogenase; a diamine transporter, a dicarboxylate transporter,S-adenosylmethionine synthetase; and/or a multidrug transporter.
 20. Amethod for biosynthesizing a product selected from the group consistingof adipic acid, 6-aminohexanoate, 6-hydroxhexanoate,hexamethylenediamine, caprolactam and 1,6-hexanediol, said methodcomprising enzymatically synthesizing a six carbon chain aliphaticbackbone from oxalyl-CoA and either (i) acetyl-CoA or malonyl-CoA viatwo cycles of methyl ester shielded carbon chain elongation or (ii)malonyl-[acp] via two cycles of methyl-ester shielded carbon chainelongation, and enzymatically forming two terminal functional groupsselected from the group consisting of carboxyl, amine, and hydroxylgroups in said backbone, thereby forming the product, wherein the methodis performed in vitro.
 21. The method of claim 20, wherein the sixcarbon chain aliphatic backbone is adipyl-[acp] or adipyl-CoA.
 22. Themethod of claim 20, wherein a polypeptide having the activity of amalonyl-[acp] O-methyltransferase converts oxalyl-CoA to oxalyl-CoAmethyl ester.
 23. The method of claim 22, wherein each of said twocycles of carbon chain elongation comprises using a polypeptide havingthe activity of (i) a β-ketoacyl-[acp] synthase or a β-ketothiolase,(ii) a 3-oxoacyl-[acp] reductase, an acetoacetyl-CoA reductase, a3-hydroxyacyl-CoA dehydrogenase or a 3-hydroxybutyryl-CoA dehydrogenase,(iii) an enoyl-CoA hydratase or a 3-hydroxyacyl-[acp] dehydratase, and(iv) an enoyl-[acp] reductase or a trans-2-enoyl-CoA reductase toproduce adipyl-CoA methyl ester or adipyl-[acp] methyl ester.
 24. Themethod of claim 23, wherein a polypeptide having the activity of apimeloyl-[acp] methyl ester methylesterase removes the methyl group fromadipyl-CoA methyl ester or adipyl-[acp] methyl ester.
 25. The method ofclaim 22, wherein the polypeptide having the activity of a malonyl-[acp]O-methyltransferase has at least 70% sequence identity to the amino acidsequence set forth in SEQ ID NO:
 16. 26. The method of claim 24, whereinthe polypeptide having the activity of a pimeloyl-[acp] methyl estermethylesterase has at least 70% sequence identity to the amino acidsequence set forth in SEQ ID NO:
 17. 27. The method of claim 20, whereina polypeptide having the activity of a 6-hydroxyhexanoate dehydrogenase,a 5-hydroxypentanoate dehydrogenase, a 4-hydroxybutyrate dehydratase, oran alcohol dehydrogenase enzymatically forms a hydroxyl group; apolypeptide having the activity of a thioesterase, an aldehydedehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoatedehydrogenase, a glutaconate CoA-transferase, or a reversiblesuccinyl-CoA ligase enzymatically forms a terminal carboxyl group; or apolypeptide having the activity of a ω-transaminase or a deacetylaseenzymatically forms an amine group.
 28. The method of claim 27, whereinsaid polypeptide having the activity of a thioesterase has at least 70%sequence identity to the amino acid sequence set forth in SEQ ID NO: 1;or said polypeptide having the activity of a ω-transaminase has at least70% sequence identity to any one of the amino acid sequences set forthin SEQ ID NOs: 8-13.
 29. The method of claim 20, wherein a polypeptidehaving the activity of a carboxylate reductase, enhanced by apolypeptide having the activity of a phosphopantetheinyl transferase,forms a terminal aldehyde group as an intermediate in forming theproduct.
 30. The method of claim 29, wherein said polypeptide having theactivity of a carboxylate reductase has at least 70% sequence identityto any one of the amino acid sequences set forth in SEQ ID NOs. 3-7.